2PPB

Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the ntp substrate analog and antibiotic streptolydigin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
I [auth C]	d2ppbc_	Multi-domain proteins (alpha and beta)	beta and beta-prime subunits of DNA dependent RNA-polymerase	beta and beta-prime subunits of DNA dependent RNA-polymerase	RNA-polymerase beta	automated matches	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
N [auth M]	d2ppbm_	Multi-domain proteins (alpha and beta)	beta and beta-prime subunits of DNA dependent RNA-polymerase	beta and beta-prime subunits of DNA dependent RNA-polymerase	RNA-polymerase beta	automated matches	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
J [auth D]	d2ppbd_	Multi-domain proteins (alpha and beta)	beta and beta-prime subunits of DNA dependent RNA-polymerase	beta and beta-prime subunits of DNA dependent RNA-polymerase	RNA-polymerase beta-prime	automated matches	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
O [auth N]	d2ppbn_	Multi-domain proteins (alpha and beta)	beta and beta-prime subunits of DNA dependent RNA-polymerase	beta and beta-prime subunits of DNA dependent RNA-polymerase	RNA-polymerase beta-prime	automated matches	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
K [auth E]	d2ppbe_	All alpha proteins	RPB6/omega subunit-like	RPB6/omega subunit-like	RNA polymerase omega subunit	RNA polymerase omega subunit	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
P [auth O]	d2ppbo_	All alpha proteins	RPB6/omega subunit-like	RPB6/omega subunit-like	RNA polymerase omega subunit	RNA polymerase omega subunit	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G [auth A]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8039604	3001655	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8039607	3001500	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8039604	3001655	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8039607	3001500	SCOP2B (2022-06-29)
L [auth K]	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8039607	3001500	SCOP2B (2022-06-29)
L [auth K]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8039604	3001655	SCOP2B (2022-06-29)
M [auth L]	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8039607	3001500	SCOP2B (2022-06-29)
M [auth L]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8039604	3001655	SCOP2B (2022-06-29)
I [auth C]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039611	3001330	SCOP2B (2022-06-29)
N [auth M]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039611	3001330	SCOP2B (2022-06-29)
J [auth D]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039613	3001330	SCOP2B (2022-06-29)
O [auth N]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039613	3001330	SCOP2B (2022-06-29)
K [auth E]	SCOP2B Superfamily	RPB6/omega subunit-like	8039612	3000189	SCOP2B (2022-06-29)
P [auth O]	SCOP2B Superfamily	RPB6/omega subunit-like	8039612	3000189	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)
G [auth A]	RNA_pol_L	e2ppbA1	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	ECOD (1.6)
G [auth A]	RNA_pol_A_bac	e2ppbA2	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	ECOD (1.6)
H [auth B]	RNA_pol_L	e2ppbB1	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	ECOD (1.6)
H [auth B]	RNA_pol_A_bac	e2ppbB2	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	ECOD (1.6)
L [auth K]	RNA_pol_L	e2ppbK1	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	ECOD (1.6)
L [auth K]	RNA_pol_A_bac	e2ppbK2	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	ECOD (1.6)
M [auth L]	RNA_pol_L	e2ppbL1	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	ECOD (1.6)
M [auth L]	RNA_pol_A_bac	e2ppbL2	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	ECOD (1.6)
I [auth C]	RNA_pol_Rpb2_6_3rd_3	e2ppbC9	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_3	ECOD (1.6)
I [auth C]	RNA_pol_Rpb2_6_1st_1	e2ppbC2	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_1st_1	ECOD (1.6)
I [auth C]	RNA_pol_Rpb2_6_2nd	e2ppbC8	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	ECOD (1.6)
I [auth C]	RNA_pol_Rpb2_3	e2ppbC4	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)
I [auth C]	RNA_pol_Rpb2_1	e2ppbC5	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)
I [auth C]	RNA_pol_Rpb2_45	e2ppbC6	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	ECOD (1.6)
I [auth C]	RNA_pol_Rpb2_7	e2ppbC7	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)
N [auth M]	RNA_pol_Rpb2_6_3rd_3	e2ppbM9	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_3	ECOD (1.6)
N [auth M]	RNA_pol_Rpb2_6_1st_1	e2ppbM2	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_1st_1	ECOD (1.6)
N [auth M]	RNA_pol_Rpb2_6_2nd	e2ppbM8	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	ECOD (1.6)
N [auth M]	RNA_pol_Rpb2_3	e2ppbM4	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)
N [auth M]	RNA_pol_Rpb2_1	e2ppbM5	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)
N [auth M]	RNA_pol_Rpb2_45	e2ppbM6	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	ECOD (1.6)
N [auth M]	RNA_pol_Rpb2_7	e2ppbM7	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)
J [auth D]	RNA_pol_Rpb1_2	e2ppbD9	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
J [auth D]	PRK00566_1st	e2ppbD10	A: alpha arrays	X: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology)	H: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology)	T: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit	F: PRK00566_1st	ECOD (1.6)
J [auth D]	PRK00566_2nd	e2ppbD8	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: PRK00566_2nd	ECOD (1.6)
J [auth D]	biotinyl_domain_like	e2ppbD1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: biotinyl_domain_like	ECOD (1.6)
J [auth D]	RnfC_N_like_1	e2ppbD7	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RnfC_N_like_1	ECOD (1.6)
J [auth D]	RNA_pol_Rpb1_5_2nd	e2ppbD2	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_Rpb1_5_2nd	ECOD (1.6)
J [auth D]	RNA_pol_Rpb1_1	e2ppbD3	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)
J [auth D]	RNA_pol_Rpb1_5_3rd	e2ppbD4	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)
J [auth D]	RNA_pol_Rpb1_4	e2ppbD5	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)
J [auth D]	RNA_pol_Rpb1_3	e2ppbD6	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)
O [auth N]	RNA_pol_Rpb1_2	e2ppbN2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
O [auth N]	PRK00566_1st	e2ppbN4	A: alpha arrays	X: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology)	H: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology)	T: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit	F: PRK00566_1st	ECOD (1.6)
O [auth N]	PRK00566_2nd	e2ppbN40	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: PRK00566_2nd	ECOD (1.6)
O [auth N]	biotinyl_domain_like	e2ppbN39	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: biotinyl_domain_like	ECOD (1.6)
O [auth N]	RnfC_N_like_1	e2ppbN38	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RnfC_N_like_1	ECOD (1.6)
O [auth N]	RNA_pol_Rpb1_1	e2ppbN37	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)
O [auth N]	RNA_pol_Rpb1_5_3rd	e2ppbN42	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)
O [auth N]	RNA_pol_Rpb1_4	e2ppbN41	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)
O [auth N]	RNA_pol_Rpb1_3	e2ppbN35	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)
K [auth E]	RNA_pol_Rpb6	e2ppbE1	A: alpha arrays	X: RPB6/omega subunit-like (From Homology)	H: RPB6/omega subunit-like	T: RNA polymerase omega subunit	F: RNA_pol_Rpb6	ECOD (1.6)
P [auth O]	RNA_pol_Rpb6	e2ppbO1	A: alpha arrays	X: RPB6/omega subunit-like (From Homology)	H: RPB6/omega subunit-like	T: RNA polymerase omega subunit	F: RNA_pol_Rpb6	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G [auth A]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
G [auth A]	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)
H [auth B]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
H [auth B]	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)
L [auth K]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
L [auth K]	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)
M [auth L]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
M [auth L]	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)
I [auth C]	2.40.270.10	Mainly Beta	Beta Barrel	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
I [auth C]	3.90.1100.10	Alpha Beta	Alpha-Beta Complex	Rna Polymerase Beta Subunit	Chain: C,domain 2	CATH (4.3.0)
I [auth C]	3.90.1110.10	Alpha Beta	Alpha-Beta Complex	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
I [auth C]	2.30.150.10	Mainly Beta	Roll	Rna Polymerase Beta Subunit	Chain: C, domain 4	CATH (4.3.0)
I [auth C]	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
I [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)
N [auth M]	2.40.270.10	Mainly Beta	Beta Barrel	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
N [auth M]	3.90.1100.10	Alpha Beta	Alpha-Beta Complex	Rna Polymerase Beta Subunit	Chain: C,domain 2	CATH (4.3.0)
N [auth M]	3.90.1110.10	Alpha Beta	Alpha-Beta Complex	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
N [auth M]	2.30.150.10	Mainly Beta	Roll	Rna Polymerase Beta Subunit	Chain: C, domain 4	CATH (4.3.0)
N [auth M]	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
N [auth M]	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
J [auth D]	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
J [auth D]	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
J [auth D]	1.10.274.100	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (4.3.0)
J [auth D]	1.10.132.30	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)
O [auth N]	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
O [auth N]	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
O [auth N]	1.10.40.90	Mainly Alpha	Orthogonal Bundle	Ribonucleotide Reductase Protein R1	domain 1	CATH (4.3.0)
O [auth N]	1.10.132.30	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)
O [auth N]	3.90.105.10	Alpha Beta	Alpha-Beta Complex	Molybdopterin biosynthesis moea protein, domain 2	Molybdopterin biosynthesis moea protein, domain 2	CATH (4.3.0)
O [auth N]	3.30.60.280	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
K [auth E]	3.90.940.10	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RNA polymerase subunit, RPB6/omega	CATH (4.3.0)
P [auth O]	3.90.940.10	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RNA polymerase subunit, RPB6/omega	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth A], H [auth B], L [auth K], M [auth L]	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
G [auth A], H [auth B], L [auth K], M [auth L]	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
I [auth C], N [auth M]	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
I [auth C], N [auth M]	PF10385	RNA polymerase beta subunit external 1 domain (RNA_pol_Rpb2_45)	RNA polymerase beta subunit external 1 domain	RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between ...	RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region [1].	Domain
I [auth C], N [auth M]	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
I [auth C], N [auth M]	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
I [auth C], N [auth M]	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
I [auth C], N [auth M]	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
J [auth D], O [auth N]	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
J [auth D], O [auth N]	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
J [auth D], O [auth N]	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
J [auth D], O [auth N]	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
J [auth D], O [auth N]	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
K [auth E], P [auth O]	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth G], D [auth X]	DNA (5'-D(PCPCPCPTPGPTPCPTPGPGPCPGPTPTPCPGPCPGPCPGPCPCP*G)-3')	-	-	-
B [auth H], E [auth Y]	RNA (5'-R(PGPAPGPUPCPUPGPCPGPGPCPGPCPGPCPG)-3')	-	-	-
C [auth I], F [auth Z]	DNA (5'-D(APAPCPGPCPCPAPGPAPCPAPGPGPG)-3')	-	-	-
G [auth A], H [auth B], L [auth K], M [auth L]	DNA-directed RNA polymerase alpha chain	DNA binding binding nucleic acid binding protein binding protein dimerization activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
I [auth C], N [auth M]	DNA-directed RNA polymerase beta chain	DNA binding binding nucleic acid binding ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding	-	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
J [auth D], O [auth N]	DNA-directed RNA polymerase beta' chain	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding transition metal ion binding zinc ion binding	-	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
K [auth E], P [auth O]	DNA-directed RNA polymerase omega chain	DNA binding binding nucleic acid binding	-	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth A], H [auth B], L [auth K], M [auth L]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
G [auth A], H [auth B], L [auth K], M [auth L]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
G [auth A], H [auth B], L [auth K], M [auth L]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
G [auth A], H [auth B], L [auth K], M [auth L]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
G [auth A], H [auth B], L [auth K], M [auth L]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
G [auth A], H [auth B], L [auth K], M [auth L]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
I [auth C], N [auth M]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
I [auth C], N [auth M]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
I [auth C], N [auth M]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
I [auth C], N [auth M]	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
I [auth C], N [auth M]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
I [auth C], N [auth M]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
I [auth C], N [auth M]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
I [auth C], N [auth M]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
I [auth C], N [auth M]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
I [auth C], N [auth M]	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
I [auth C], N [auth M]	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
I [auth C], N [auth M]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
I [auth C], N [auth M]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
J [auth D], O [auth N]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
J [auth D], O [auth N]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
J [auth D], O [auth N]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
J [auth D], O [auth N]	IPR012754	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Family
J [auth D], O [auth N]	IPR048566	DNA-directed RNA polymerase subunit beta', hybrid domain	Domain
J [auth D], O [auth N]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
J [auth D], O [auth N]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
J [auth D], O [auth N]	IPR000722	RNA polymerase, alpha subunit	Domain
J [auth D], O [auth N]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
J [auth D], O [auth N]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
J [auth D], O [auth N]	IPR006592	RNA polymerase, N-terminal	Domain
J [auth D], O [auth N]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
K [auth E], P [auth O]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
K [auth E], P [auth O]	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
K [auth E], P [auth O]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family