Annotations: 3H3V

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8042682	3001330	SCOP2B (2022-06-29)
J [auth K]	SCOP2B Superfamily	RNA polymerase subunit RPB10	8042692	3001213	SCOP2B (2022-06-29)
K [auth L]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8042694	3001655	SCOP2B (2022-06-29)
L [auth M]	SCOP2B Superfamily	RNA polymerase subunits	8042695	3001823	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8042684	3001330	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8042685	3001655	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8042687	3001500	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	Eukaryotic RPB5 N-terminal domain	8044454	3000444	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	RPB5-like RNA polymerase subunit	8035939	3001722	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	RPB6/omega subunit-like	8042688	3000189	SCOP2B (2022-06-29)
G [auth H]	SCOP2B Superfamily	Nucleic acid-binding proteins	8044251	3000135	SCOP2B (2022-06-29)
G [auth H]	SCOP2B Superfamily	N-terminal, heterodimerisation domain of RBP7 (RpoE)	8044252	3001137	SCOP2B (2022-06-29)
H [auth I]	SCOP2B Superfamily	RBP8/CHS5 N-terminal domain-like	8041967	3002702	SCOP2B (2022-06-29)
H [auth I]	SCOP2B Superfamily	RBP8/CHS5 N-terminal domain-like	8093392	3002702	SCOP2B (2022-06-29)
I [auth J]	SCOP2B Superfamily	Zinc beta-ribbon	8042689	3001238	SCOP2B (2022-06-29)
I [auth J]	SCOP2B Superfamily	Zinc beta-ribbon	8042690	3001238	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	RNA_pol_Rpb1_2	e3h3vB5	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
A [auth B]	RNA_pol_Rpb1_2_1	e3h3vB2	A: a+b two layers	X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: RNA_pol_Rpb1_2_1	ECOD (1.6)
A [auth B]	RNA_pol_Rpb1_7	e3h3vB8	A: a+b two layers	X: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	H: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	T: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_7	ECOD (1.6)
A [auth B]	RNA_pol_Rpb1_7_1	e3h3vB6	A: a+b two layers	X: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	H: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	T: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_7_1	ECOD (1.6)
A [auth B]	RNA_pol_Rpb1_1	e3h3vB4	A: a+b complex topology	X: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	H: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	T: N-terminal domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_1	ECOD (1.6)
A [auth B]	RNA_pol_Rpb1_5_3rd	e3h3vB1	A: a+b complex topology	X: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: central helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_5_3rd	ECOD (1.6)
A [auth B]	RNA_pol_Rpb1_6	e3h3vB7	A: a+b complex topology	X: helical domain in yeast RNA-polymerases	H: third helical domain in yeast RNA-polymerase II beta-prime subunit (From Topology)	T: third helical domain in yeast RNA-polymerase II beta-prime subunit	F: RNA_pol_Rpb1_6	ECOD (1.6)
A [auth B]	RNA_pol_Rpb1_4	e3h3vB3	A: a+b complex topology	X: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: second helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_4	ECOD (1.6)
A [auth B]	RNA_pol_Rpb1_3	e3h3vB9	A: a+b complex topology	X: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: first helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_3	ECOD (1.6)
J [auth K]	RNA_pol_N	e3h3vK1	A: alpha arrays	X: HTH	H: RPB10 (From Topology)	T: RPB10	F: RNA_pol_N	ECOD (1.6)
K [auth L]	RNA_pol_L_2	e3h3vL1	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L_2	ECOD (1.6)
L [auth M]	DNA_RNApol_7kD	e3h3vM1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: DNA_RNApol_7kD	ECOD (1.6)
B [auth C]	RNA_pol_Rpb2_6_3rd_2	e3h3vC5	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_2	ECOD (1.6)
B [auth C]	RNA_pol_Rpb2_6_2nd_1	e3h3vC4	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RNA_pol_Rpb2_6_2nd_1	ECOD (1.6)
B [auth C]	RNA_pol_Rpb2_3	e3h3vC3	A: a+b complex topology	X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: N-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_3	ECOD (1.6)
B [auth C]	RNA_pol_Rpb2_1	e3h3vC7	A: a+b complex topology	X: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: insertion domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_1	ECOD (1.6)
B [auth C]	RNA_pol_Rpb2_45_1	e3h3vC6	A: a+b complex topology	X: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: barrel domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_45_1	ECOD (1.6)
B [auth C]	RNA_pol_Rpb2_7	e3h3vC1	A: a+b complex topology	X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: C-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_7	ECOD (1.6)
B [auth C]	RNA_pol_Rpb2_4	e3h3vC2	A: a+b complex topology	X: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	H: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	T: inserted a+b domain in yeast RNA polymerase beta subunit	F: RNA_pol_Rpb2_4	ECOD (1.6)
C [auth D]	RNA_pol_L_1	e3h3vD3	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L_1	ECOD (1.6)
C [auth D]	RNA_pol_A_bac_1	e3h3vD4	A: a+b complex topology	X: Ribosomal protein TL5/L25 C-terminal domain-like	H: Insert subdomain of RNA polymerase alpha subunit (From Topology)	T: Insert subdomain of RNA polymerase alpha subunit	F: RNA_pol_A_bac_1	ECOD (1.6)
D [auth E]	RNA_pol_Rpb4	e3h3vE1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: RNA_pol_Rpb4	ECOD (1.6)
E [auth F]	RNA_pol_Rpb5_C	e3h3vF1	A: a+b two layers	X: RPB5-like RNA polymerase subunit (From Topology)	H: RPB5-like RNA polymerase subunit (From Topology)	T: RPB5-like RNA polymerase subunit	F: RNA_pol_Rpb5_C	ECOD (1.6)
E [auth F]	RNA_pol_Rpb5_N	e3h3vF2	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Eukaryotic RPB5 N-terminal domain (From Topology)	T: Eukaryotic RPB5 N-terminal domain	F: RNA_pol_Rpb5_N	ECOD (1.6)
F [auth G]	RNA_pol_Rpb6_1	e3h3vG1	A: alpha arrays	X: RPB6/omega subunit-like (From Homology)	H: RPB6/omega subunit-like	T: RPB6	F: RNA_pol_Rpb6_1	ECOD (1.6)
G [auth H]	S1_1	e3h3vH3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
G [auth H]	SHS2_Rpb7-N	e3h3vH4	A: a+b two layers	X: Dodecin subunit-like	H: Flavin-binding protein dodecin-like (From Topology)	T: Flavin-binding protein dodecin-like	F: SHS2_Rpb7-N	ECOD (1.6)
H [auth I]	RNA_pol_Rpb8	e3h3vI1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: RNA_pol_Rpb8	ECOD (1.6)
I [auth J]	RNA_POL_M_15KD	e3h3vJ1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: RNA_POL_M_15KD	ECOD (1.6)
I [auth J]	TFIIS_C	e3h3vJ2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: TFIIS_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
A [auth B]	3.30.1490.180	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A [auth B]	1.10.274.100	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (4.3.0)
A [auth B]	1.10.132.30	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)
A [auth B]	3.30.1360.140	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
J [auth K]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
K [auth L]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
L [auth M]	2.20.28.30	Mainly Beta	Single Sheet	Rubrerythrin, domain 2	RNA polymerase ii, chain L	CATH (4.3.0)
B [auth C]	3.90.1110.10	Alpha Beta	Alpha-Beta Complex	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
B [auth C]	3.90.1070.20	Alpha Beta	Alpha-Beta Complex	Hypothetical Protein Ta0175	Chain: A, domain 2	CATH (4.3.0)
B [auth C]	2.40.270.10	Mainly Beta	Beta Barrel	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
B [auth C]	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
B [auth C]	3.90.1800.10	Alpha Beta	Alpha-Beta Complex	DCoH-like	RNA polymerase alpha subunit dimerisation domain	CATH (4.3.0)
C [auth D]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
C [auth D]	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)
D [auth E]	1.20.1250.40	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
E [auth F]	3.40.1340.10	Alpha Beta	3-Layer(aba) Sandwich	Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide	Chain: A	CATH (4.3.0)
E [auth F]	3.90.940.20	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RPB5-like RNA polymerase subunit	CATH (4.3.0)
F [auth G]	3.90.940.10	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RNA polymerase subunit, RPB6/omega	CATH (4.3.0)
G [auth H]	3.30.1490.120	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
G [auth H]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
H [auth I]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
I [auth J]	2.20.25.10	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF00623	RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)	RNA polymerase Rpb1, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].	Domain
A [auth B]	PF04990	RNA polymerase Rpb1, domain 7 (RNA_pol_Rpb1_7)	RNA polymerase Rpb1, domain 7	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile modu ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (Pfam:PF04561) [1,2].	Domain
A [auth B]	PF05000	RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)	RNA polymerase Rpb1, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].	Domain
A [auth B]	PF04983	RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)	RNA polymerase Rpb1, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].	Domain
A [auth B]	PF04992	RNA polymerase Rpb1, domain 6 (RNA_pol_Rpb1_6)	RNA polymerase Rpb1, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile modu ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [1,2]. This family appears to be specific to the largest subunit of RNA polymerase II.	Domain
A [auth B]	PF04998	RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)	RNA polymerase Rpb1, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].	Domain
A [auth B]	PF04997	RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)	RNA polymerase Rpb1, domain 1	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp dom ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2].	Domain
J [auth K]	PF01194	RNA polymerases N / 8 kDa subunit (RNA_pol_N)	RNA polymerases N / 8 kDa subunit		Domain
K [auth L]	PF13656	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11.	Domain
L [auth M]	PF03604	DNA directed RNA polymerase, 7 kDa subunit (Zn_ribbon_RPAB4)	DNA directed RNA polymerase, 7 kDa subunit		Domain
B [auth C]	PF04561	RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)	RNA polymerase Rpb2, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).	Domain
B [auth C]	PF04560	RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)	RNA polymerase Rpb2, domain 7	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA p ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1].	Domain
B [auth C]	PF04565	RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)	RNA polymerase Rpb2, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1].	Domain
B [auth C]	PF04566	RNA polymerase Rpb2, domain 4 (RNA_pol_Rpb2_4)	RNA polymerase Rpb2, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain [1].	Domain
B [auth C]	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
B [auth C]	PF00562	RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)	RNA polymerase Rpb2, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).	Domain
B [auth C]	PF04567	RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5)	RNA polymerase Rpb2, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain [1].	Domain
C [auth D]	PF01193	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.	Domain
C [auth D]	PF01000	RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)	RNA polymerase Rpb3/RpoA insert domain	Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal	Domain
D [auth E]	PF03874	RNA polymerase Rpb4 (RNA_pol_Rpb4)	RNA polymerase Rpb4	-	Family
E [auth F]	PF01191	RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C)	RNA polymerase Rpb5, C-terminal domain	The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain.	Domain
E [auth F]	PF03871	RNA polymerase Rpb5, N-terminal domain (RNA_pol_Rpb5_N)	RNA polymerase Rpb5, N-terminal domain	Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA p ...	Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure [3]. This module is important for positioning the downstream DNA.	Domain
F [auth G]	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
G [auth H]	PF03876	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N)	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397	Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at leas ...	Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA [2]. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction [3].	Domain
G [auth H]	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain
H [auth I]	PF03870	RNA polymerase Rpb8 (RNA_pol_Rpb8)	RNA polymerase Rpb8	-	Family
I [auth J]	PF02150	RNA polymerases M/15 Kd subunit (Zn_ribbon_RPB9)	RNA polymerases M/15 Kd subunit		Domain
I [auth J]	PF01096	Transcription factor S-II (TFIIS) (Zn_ribbon_TFIIS)	Transcription factor S-II (TFIIS)		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	DNA-directed RNA polymerase II subunit RPB1	DNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process translesion synthesis cellular response to stimulus postreplication repair response to stimulus DNA metabolic process DNA synthesis involved in DNA repair cellular response to stress DNA damage response response to stress DNA biosynthetic process DNA repair RNA-templated transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule RNA polymerase II, holoenzyme protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen nucleoplasm RNA polymerase II, core complex catalytic complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
J [auth K]	DNA-directed RNA polymerases I, II, and III subunit RPABC5	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription by RNA polymerase III nucleolar large rRNA transcription by RNA polymerase I transcription by RNA polymerase I rRNA transcription rRNA metabolic process DNA-templated transcription termination termination of RNA polymerase I transcription RNA-templated transcription termination of RNA polymerase III transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription initiation at RNA polymerase III promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I transcription initiation at RNA polymerase I promoter	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex
K [auth L]	DNA-directed RNA polymerase II subunit RPB11	DNA binding binding nucleic acid binding protein binding protein dimerization activity	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process DNA-templated transcription termination DNA-templated transcription transcription by RNA polymerase II termination of RNA polymerase II transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
L [auth M]	DNA-directed RNA polymerases I, II, and III subunit RPABC4	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription by RNA polymerase III nucleolar large rRNA transcription by RNA polymerase I transcription by RNA polymerase I rRNA transcription rRNA metabolic process DNA-templated transcription termination termination of RNA polymerase I transcription RNA-templated transcription termination of RNA polymerase III transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription initiation at RNA polymerase III promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I transcription initiation at RNA polymerase I promoter	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex RNA polymerase I complex nuclear protein-containing complex transferase complex catalytic complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex cytoplasm peroxisome microbody
M [auth N]	5'-D(APGPCPTPCPAPAPGPTPAPGPCPTPGPCPTPTPTPAPTPTPGPCPAPTPT)-3'	-	-	-
N [auth P]	5'-D(CPAPGPCPTPAPCPTPTPGPAPGPCPT)-3'	-	-	-
O [auth T]	5'-R(UPGPCPAPUPUPUPCPGPCPAPAPUPAPAPA)-3'	-	-	-
B [auth C]	DNA-directed RNA polymerase II subunit RPB2	ribonucleoside binding binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding DNA binding nucleic acid binding RNA binding mRNA binding cation binding ion binding metal ion binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process RNA-templated transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule RNA polymerase II, holoenzyme protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen nucleoplasm RNA polymerase II, core complex catalytic complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
C [auth D]	DNA-directed RNA polymerase II subunit RPB3	DNA binding binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding protein dimerization activity DNA binding binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding protein dimerization activity cation binding ion binding metal ion binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process DNA-templated transcription termination DNA-templated transcription transcription by RNA polymerase II termination of RNA polymerase II transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
D [auth E]	DNA-directed RNA polymerase II subunit RPB4	protein binding binding translation initiation factor binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process DNA-templated transcription initiation DNA-templated transcription transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process translational initiation protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of translational initiation regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process translation regulation of gene expression positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process positive regulation of translational initiation regulation of metabolic process mRNA processing mRNA metabolic process RNA processing negative regulation of biological process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process positive regulation of nucleobase-containing compound metabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process RNA destabilization nuclear-transcribed mRNA catabolic process regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RPB4-RPB7 complex cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle cytoplasm supramolecular complex P-body
E [auth F]	DNA-directed RNA polymerases I, II, and III subunit RPABC1	DNA binding binding nucleic acid binding	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription by RNA polymerase III nucleolar large rRNA transcription by RNA polymerase I transcription by RNA polymerase I rRNA transcription rRNA metabolic process DNA-templated transcription termination termination of RNA polymerase I transcription RNA-templated transcription termination of RNA polymerase III transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription initiation at RNA polymerase III promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I transcription initiation at RNA polymerase I promoter	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex
F [auth G]	DNA-directed RNA polymerases I, II, and III subunit RPABC2	DNA binding binding nucleic acid binding	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription by RNA polymerase III nucleolar large rRNA transcription by RNA polymerase I transcription by RNA polymerase I rRNA transcription rRNA metabolic process DNA-templated transcription termination termination of RNA polymerase I transcription RNA-templated transcription termination of RNA polymerase III transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription initiation at RNA polymerase III promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I transcription initiation at RNA polymerase I promoter	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex cytoplasm
G [auth H]	DNA-directed RNA polymerase II subunit RPB7	protein binding binding translation initiation factor binding RNA binding nucleic acid binding single-stranded RNA binding DNA binding single-stranded DNA binding	regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process nucleobase-containing compound biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process RNA-templated transcription DNA-templated transcription initiation DNA-templated transcription transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process translational initiation protein metabolic process positive regulation of cellular process regulation of translational initiation regulation of protein metabolic process translation positive regulation of gene expression regulation of translation positive regulation of translational initiation regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay mRNA destabilization regulation of mRNA catabolic process RNA destabilization regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process positive regulation of nuclear-transcribed mRNA poly(A) tail shortening nuclear-transcribed mRNA poly(A) tail shortening regulation of nuclear-transcribed mRNA poly(A) tail shortening	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RPB4-RPB7 complex cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle cytoplasm supramolecular complex P-body
H [auth I]	DNA-directed RNA polymerases I, II, and III subunit RPABC3	DNA binding binding nucleic acid binding	nucleolar large rRNA transcription by RNA polymerase I RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I rRNA transcription nucleolar large rRNA transcription by RNA polymerase I RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I rRNA transcription metabolic process cellular process macromolecule metabolic process rRNA metabolic process DNA-templated transcription termination termination of RNA polymerase I transcription RNA-templated transcription termination of RNA polymerase III transcription transcription by RNA polymerase III DNA-templated transcription initiation transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter transcription initiation at RNA polymerase III promoter cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular component organization or biogenesis transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription initiation at RNA polymerase I promoter	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex
I [auth J]	DNA-directed RNA polymerase II subunit RPB9	binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding transition metal ion binding zinc ion binding binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process DNA-templated transcription initiation DNA-templated transcription transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation maintenance of transcriptional fidelity during transcription elongation maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II cellular response to stimulus response to stimulus transcription-coupled nucleotide-excision repair DNA metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress DNA repair	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen RNA polymerase II, holoenzyme protein-containing complex nuclear protein-containing complex transferase complex nucleoplasm RNA polymerase II, core complex catalytic complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
A [auth B]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
A [auth B]	IPR007075	RNA polymerase Rpb1, domain 6	Domain
A [auth B]	IPR000684	RNA polymerase II, heptapeptide repeat, eukaryotic	Repeat
A [auth B]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
A [auth B]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
A [auth B]	IPR006592	RNA polymerase, N-terminal	Domain
A [auth B]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
A [auth B]	IPR007073	RNA polymerase Rpb1, domain 7	Domain
A [auth B]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
A [auth B]	IPR038593	RNA polymerase Rpb1, domain 7 superfamily	Homologous Superfamily
A [auth B]	IPR000722	RNA polymerase, alpha subunit	Domain
A [auth B]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
A [auth B]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
J [auth K]	IPR020789	RNA polymerases, subunit N, zinc binding site	Binding Site
J [auth K]	IPR000268	DNA-directed RNA polymerase subunit RPABC5/Rpb10	Family
J [auth K]	IPR023580	RNA polymerase subunit RPB10	Homologous Superfamily
K [auth L]	IPR009025	DNA-directed RNA polymerase, RBP11-like dimerisation domain	Domain
K [auth L]	IPR037685	RNA polymerase RBP11	Family
K [auth L]	IPR022905	DNA-directed RNA polymerase subunit Rpo11-like	Family
K [auth L]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
K [auth L]	IPR008193	DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site	Conserved Site
L [auth M]	IPR006591	RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4	Family
L [auth M]	IPR029040	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Homologous Superfamily
L [auth M]	IPR039747	DNA-directed RNA polymerases I, II, and III subunit RPABC4	Family
B [auth C]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
B [auth C]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
B [auth C]	IPR007646	RNA polymerase Rpb2, domain 4	Domain
B [auth C]	IPR007647	RNA polymerase Rpb2, domain 5	Domain
B [auth C]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
B [auth C]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
B [auth C]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
B [auth C]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
B [auth C]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
B [auth C]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
B [auth C]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
B [auth C]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
C [auth D]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
C [auth D]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
C [auth D]	IPR050518	Archaeal Rpo3/Eukaryotic RPB3 RNA Polymerase Subunit	Family
C [auth D]	IPR022842	DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1	Family
C [auth D]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
C [auth D]	IPR001514	DNA-directed RNA polymerase, 30-40kDa subunit, conserved site	Conserved Site
C [auth D]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
D [auth E]	IPR005574	RNA polymerase subunit Rpb4/RPC9	Family
D [auth E]	IPR010997	HRDC-like superfamily	Homologous Superfamily
D [auth E]	IPR006590	RNA polymerase Rpb4/RPC9, core	Domain
D [auth E]	IPR038324	Rpb4/RPC9 superfamily	Homologous Superfamily
D [auth E]	IPR045222	DNA-directed RNA polymerase II subunit Rpb4-like	Family
E [auth F]	IPR036710	RNA polymerase Rpb5, N-terminal domain superfamily	Homologous Superfamily
E [auth F]	IPR014381	DNA-directed RNA polymerase subunit Rpo5/Rpb5	Family
E [auth F]	IPR035913	RPB5-like RNA polymerase subunit superfamily	Homologous Superfamily
E [auth F]	IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	Domain
E [auth F]	IPR020608	RNA polymerase, subunit H/Rpb5, conserved site	Conserved Site
E [auth F]	IPR005571	RNA polymerase, Rpb5, N-terminal	Domain
F [auth G]	IPR028363	DNA-directed RNA polymerase, subunit RPB6	Family
F [auth G]	IPR006111	Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit	Family
F [auth G]	IPR020708	DNA-directed RNA polymerase, 14-18kDa subunit, conserved site	Conserved Site
F [auth G]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
F [auth G]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
G [auth H]	IPR003029	S1 domain	Domain
G [auth H]	IPR045113	RNA polymerase subunit Rpb7-like	Family
G [auth H]	IPR005576	RNA polymerase Rpb7-like , N-terminal	Domain
G [auth H]	IPR036898	RNA polymerase Rpb7-like, N-terminal domain superfamily	Homologous Superfamily
G [auth H]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
H [auth I]	IPR005570	DNA-directed RNA polymerases I, II, and III subunit RPABC3	Family
H [auth I]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
I [auth J]	IPR001529	DNA-directed RNA polymerase II subunit RPB9-like, zinc ribbon	Domain
I [auth J]	IPR012164	DNA-directed RNA polymerase subunit/transcription factor S	Family
I [auth J]	IPR001222	Zinc finger, TFIIS-type	Domain
I [auth J]	IPR034012	Pol II subunit B9, C-terminal zinc ribbon	Domain
I [auth J]	IPR019761	DNA-directed RNA polymerase M, 15kDa subunit, conserved site	Conserved Site