4WQT

Thermus thermophilus RNA polymerase complexed with an RNA cleavage stimulating factor (a GreA/Gfh1 chimeric protein)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8039604	3001655	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8039607	3001500	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8039604	3001655	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8039607	3001500	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8039607	3001500	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8039604	3001655	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8039604	3001655	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8039607	3001500	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8039607	3001500	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8039604	3001655	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8039607	3001500	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8039604	3001655	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039611	3001330	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039611	3001330	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039611	3001330	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039613	3001330	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039613	3001330	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039613	3001330	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RPB6/omega subunit-like	8039612	3000189	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	RPB6/omega subunit-like	8039612	3000189	SCOP2B (2022-06-29)
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)
A	RNA_pol_L	e4wqtA1	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)
A	RNA_pol_A_bac	e4wqtA2	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)
B	RNA_pol_L	e4wqtB2	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)
B	RNA_pol_A_bac	e4wqtB1	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)
F	RNA_pol_L	e4wqtF2	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)
F	RNA_pol_A_bac	e4wqtF1	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)
G	RNA_pol_L	e4wqtG2	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	RNA_pol_A_bac	e4wqtG1	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)
K	RNA_pol_L	e4wqtK1	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)
K	RNA_pol_A_bac	e4wqtK2	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	RNA_pol_L	e4wqtL2	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	RNA_pol_A_bac	e4wqtL1	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)
C	RNA_pol_Rpb2_6_3rd_3	e4wqtC7	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_3	ECOD (1.6)
C	RNA_pol_Rpb2_6_1st_1	e4wqtC3	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)
C	RNA_pol_Rpb2_6_2nd	e4wqtC6	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)
C	RNA_pol_Rpb2_3	e4wqtC1	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)
C	RNA_pol_Rpb2_1	e4wqtC5	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)
C	RNA_pol_Rpb2_45	e4wqtC4	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)
C	RNA_pol_Rpb2_7	e4wqtC2	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)
H	RNA_pol_Rpb2_6_3rd_3	e4wqtH7	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_3	ECOD (1.6)
H	RNA_pol_Rpb2_6_1st_1	e4wqtH4	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)
H	RNA_pol_Rpb2_6_2nd	e4wqtH6	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)
H	RNA_pol_Rpb2_3	e4wqtH3	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)
H	RNA_pol_Rpb2_1	e4wqtH5	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)
H	RNA_pol_Rpb2_45	e4wqtH1	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)
H	RNA_pol_Rpb2_7	e4wqtH2	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)
M	RNA_pol_Rpb2_6_3rd_3	e4wqtM7	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_3	ECOD (1.6)
M	RNA_pol_Rpb2_6_1st_1	e4wqtM2	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)
M	RNA_pol_Rpb2_6_2nd	e4wqtM6	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)
M	RNA_pol_Rpb2_3	e4wqtM4	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)
M	RNA_pol_Rpb2_1	e4wqtM3	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)
M	RNA_pol_Rpb2_45	e4wqtM5	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)
M	RNA_pol_Rpb2_7	e4wqtM1	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)
D	RNA_pol_Rpb1_2	e4wqtD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
D	PRK00566_1st	e4wqtD6	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)
D	PRK00566_2nd	e4wqtD7	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)
D	Biotin_lipoyl_2_like_1	e4wqtD4	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Biotin_lipoyl_2_like_1	ECOD (1.6)
D	RnfC_N_like_1	e4wqtD9	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)
D	RNA_pol_Rpb1_5_2nd	e4wqtD2	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)
D	RNA_pol_Rpb1_1	e4wqtD5	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)
D	RNA_pol_Rpb1_5_3rd	e4wqtD3	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)
D	RNA_pol_Rpb1_4	e4wqtD10	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)
D	RNA_pol_Rpb1_3	e4wqtD8	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)
I	RNA_pol_Rpb1_2	e4wqtI10	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
I	PRK00566_1st	e4wqtI8	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)
I	PRK00566_2nd	e4wqtI1	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)
I	Biotin_lipoyl_2_like_1	e4wqtI2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Biotin_lipoyl_2_like_1	ECOD (1.6)
I	RnfC_N_like_1	e4wqtI4	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)
I	RNA_pol_Rpb1_5_2nd	e4wqtI7	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)
I	RNA_pol_Rpb1_1	e4wqtI3	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)
I	RNA_pol_Rpb1_5_3rd	e4wqtI9	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)
I	RNA_pol_Rpb1_4	e4wqtI5	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)
I	RNA_pol_Rpb1_3	e4wqtI6	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)
N	RNA_pol_Rpb1_2	e4wqtN10	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
N	PRK00566_1st	e4wqtN1	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)
N	PRK00566_2nd	e4wqtN8	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)
N	Biotin_lipoyl_2_like_1	e4wqtN4	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Biotin_lipoyl_2_like_1	ECOD (1.6)
N	RnfC_N_like_1	e4wqtN6	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)
N	RNA_pol_Rpb1_5_2nd	e4wqtN5	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)
N	RNA_pol_Rpb1_1	e4wqtN3	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)
N	RNA_pol_Rpb1_5_3rd	e4wqtN2	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)
N	RNA_pol_Rpb1_4	e4wqtN7	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)
N	RNA_pol_Rpb1_3	e4wqtN9	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)
E	RNA_pol_Rpb6	e4wqtE1	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)
J	RNA_pol_Rpb6	e4wqtJ1	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)
O	RNA_pol_Rpb6	e4wqtO1	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 X]	GreA_GreB_N	e4wqtX2	A: alpha bundles	X: Long alpha-hairpin	H: GreA transcript cleavage protein, N-terminal domain (From Topology)	T: GreA transcript cleavage protein, N-terminal domain	F: GreA_GreB_N	ECOD (1.6)
P [auth X]	GreA_GreB	e4wqtX1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: GreA_GreB	ECOD (1.6)
Q [auth Y]	GreA_GreB_N	e4wqtY2	A: alpha bundles	X: Long alpha-hairpin	H: GreA transcript cleavage protein, N-terminal domain (From Topology)	T: GreA transcript cleavage protein, N-terminal domain	F: GreA_GreB_N	ECOD (1.6)
Q [auth Y]	GreA_GreB	e4wqtY1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: GreA_GreB	ECOD (1.6)
R [auth Z]	GreA_GreB_N	e4wqtZ2	A: alpha bundles	X: Long alpha-hairpin	H: GreA transcript cleavage protein, N-terminal domain (From Topology)	T: GreA transcript cleavage protein, N-terminal domain	F: GreA_GreB_N	ECOD (1.6)
R [auth Z]	GreA_GreB	e4wqtZ1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: GreA_GreB	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, F, G, K A, B, F, G, K, 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
A, B, F, G, K A, B, F, G, K, 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
C, H, 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
C, H, 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
C, H, 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
C, H, 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
C, H, M	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
C, H, 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
D, I, 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
D, I, 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
D, I, 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
D, I, 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
D, I, 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
E, J, O	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
P [auth X], Q [auth Y], R [auth Z]	PF03449	Transcription elongation factor, N-terminal (GreA_GreB_N)	Transcription elongation factor, N-terminal	This domain adopts a long alpha-hairpin structure.	Domain
P [auth X], Q [auth Y], R [auth Z]	PF01272	Transcription elongation factor, GreA/GreB, C-term (GreA_GreB)	Transcription elongation factor, GreA/GreB, C-term	This domain has an FKBP-like fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, F, G, K A, B, F, G, K, L	DNA-directed RNA polymerase subunit alpha	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
C, H, M	DNA-directed RNA polymerase subunit beta	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
D, I, N	DNA-directed RNA polymerase subunit beta'	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
E, J, O	DNA-directed RNA polymerase subunit omega	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
P [auth X], Q [auth Y], R [auth Z]	RNA cleavage stimulating factor (GreA/Gfh1 chimeric protein Gre-C1)	DNA binding binding nucleic acid binding RNA polymerase binding protein binding enzyme binding cation binding ion binding metal ion binding small molecule binding translation factor activity translation elongation factor activity translation factor activity, RNA 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 DNA-templated transcription elongation 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 DNA-templated transcription elongation biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of DNA-templated transcription elongation regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, F, G, K A, B, F, G, K, L	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
A, B, F, G, K A, B, F, G, K, L	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
A, B, F, G, K A, B, F, G, K, L	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
A, B, F, G, K A, B, F, G, K, L	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
A, B, F, G, K A, B, F, G, K, L	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
A, B, F, G, K A, B, F, G, K, L	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
C, H, M	IPR007642	RNA polymerase Rpb2, domain 2	Domain
C, H, M	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
C, H, M	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
C, H, M	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
C, H, M	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
C, H, M	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
C, H, M	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
C, H, M	IPR007645	RNA polymerase Rpb2, domain 3	Domain
C, H, M	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
C, H, M	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
C, H, M	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
C, H, M	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
C, H, M	IPR007641	RNA polymerase Rpb2, domain 7	Domain
D, I, N	IPR007066	RNA polymerase Rpb1, domain 3	Domain
D, I, N	IPR007081	RNA polymerase Rpb1, domain 5	Domain
D, I, N	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
D, I, N	IPR012754	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Family
D, I, N	IPR048566	DNA-directed RNA polymerase subunit beta', hybrid domain	Domain
D, I, N	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
D, I, N	IPR007083	RNA polymerase Rpb1, domain 4	Domain
D, I, N	IPR000722	RNA polymerase, alpha subunit	Domain
D, I, N	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
D, I, N	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
D, I, N	IPR006592	RNA polymerase, N-terminal	Domain
D, I, N	IPR007080	RNA polymerase Rpb1, domain 1	Domain
E, J, O	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
E, J, O	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
E, J, O	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
P [auth X], Q [auth Y], R [auth Z]	IPR022691	Transcription elongation factor, GreA/GreB, N-terminal	Domain
P [auth X], Q [auth Y], R [auth Z]	IPR023459	Transcription elongation factor GreA/GreB family	Family
P [auth X], Q [auth Y], R [auth Z]	IPR036805	Transcription elongation factor, GreA/GreB, N-terminal domain superfamily	Homologous Superfamily
P [auth X], Q [auth Y], R [auth Z]	IPR036953	Transcription elongation factor GreA/GreB, C-terminal domain superfamily	Homologous Superfamily
P [auth X], Q [auth Y], R [auth Z]	IPR018151	Transcription elongation factor, GreA/GreB, conserved site	Conserved Site
P [auth X], Q [auth Y], R [auth Z]	IPR001437	Transcription elongation factor, GreA/GreB, C-terminal	Domain
P [auth X], Q [auth Y], R [auth Z]	IPR022691	Transcription elongation factor, GreA/GreB, N-terminal	Domain
P [auth X], Q [auth Y], R [auth Z]	IPR023459	Transcription elongation factor GreA/GreB family	Family
P [auth X], Q [auth Y], R [auth Z]	IPR036953	Transcription elongation factor GreA/GreB, C-terminal domain superfamily	Homologous Superfamily
P [auth X], Q [auth Y], R [auth Z]	IPR018151	Transcription elongation factor, GreA/GreB, conserved site	Conserved Site
P [auth X], Q [auth Y], R [auth Z]	IPR028624	Transcription elongation factor GreA/GreB	Family
P [auth X], Q [auth Y], R [auth Z]	IPR036805	Transcription elongation factor, GreA/GreB, N-terminal domain superfamily	Homologous Superfamily
P [auth X], Q [auth Y], R [auth Z]	IPR006359	Transcription elongation factor GreA	Family
P [auth X], Q [auth Y], R [auth Z]	IPR001437	Transcription elongation factor, GreA/GreB, C-terminal	Domain