2O5I | pdb_00002o5i

Crystal structure of the T. thermophilus RNA polymerase elongation complex

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)
P [auth O]	d2o5io_	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)
K [auth E]	d2o5ie_	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)
O [auth N]	d2o5in_	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	RNA-polymerase beta-prime	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
J [auth D]	d2o5id_	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	RNA-polymerase beta-prime	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
N [auth M]	d2o5im_	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)
I [auth C]	d2o5ic_	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)
M [auth L]	d2o5il1	Alpha and beta proteins (a+b)	DCoH-like	RBP11-like subunits of RNA polymerase	RNA polymerase alpha subunit dimerisation domain	RNA polymerase alpha	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
M [auth L]	d2o5il2	Alpha and beta proteins (a+b)	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	RNA polymerase alpha subunit	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
L [auth K]	d2o5ik1	Alpha and beta proteins (a+b)	DCoH-like	RBP11-like subunits of RNA polymerase	RNA polymerase alpha subunit dimerisation domain	RNA polymerase alpha	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
L [auth K]	d2o5ik2	Alpha and beta proteins (a+b)	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	RNA polymerase alpha subunit	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
H [auth B]	d2o5ib1	Alpha and beta proteins (a+b)	DCoH-like	RBP11-like subunits of RNA polymerase	RNA polymerase alpha subunit dimerisation domain	RNA polymerase alpha	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
H [auth B]	d2o5ib2	Alpha and beta proteins (a+b)	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	RNA polymerase alpha subunit	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
G [auth A]	d2o5ia1	Alpha and beta proteins (a+b)	DCoH-like	RBP11-like subunits of RNA polymerase	RNA polymerase alpha subunit dimerisation domain	RNA polymerase alpha	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
G [auth A]	d2o5ia2	Alpha and beta proteins (a+b)	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	RNA polymerase alpha 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)
P [auth O]	SCOP2B Superfamily	RPB6/omega subunit-like	8039612	3000189	SCOP2B (2022-06-29)
K [auth E]	SCOP2B Superfamily	RPB6/omega subunit-like	8039612	3000189	SCOP2B (2022-06-29)
O [auth N]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039613	3001330	SCOP2B (2022-06-29)
J [auth D]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039613	3001330	SCOP2B (2022-06-29)
N [auth M]	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)
I [auth C]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039611	3001330	SCOP2B (2022-06-29)
I [auth C]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8039611	3001330	SCOP2B (2022-06-29)
M [auth L]	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)
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)
L [auth K]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8039604	3001655	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	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)
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)
G [auth A]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8039604	3001655	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)
P [auth O]	DAO, NAD_binding_8	e2o5iO1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: DAO, NAD_binding_8	ECOD (v294.1)
K [auth E]	DAO, NAD_binding_8	e2o5iE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: DAO, NAD_binding_8	ECOD (v294.1)
O [auth N]	Transpeptidase	e2o5iN1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Transpeptidase	ECOD (v294.1)
O [auth N]	Cobalamin_bind	e2o5iN10	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (v294.1)
J [auth D]	OMPdecase	e2o5iD1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: OMPdecase	ECOD (v294.1)
J [auth D]	Docking	e2o5iD6	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Docking	ECOD (v294.1)
N [auth M]	RNA_pol_Rpb2_2	e2o5iM4	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RNA_pol_Rpb2_2	ECOD (v294.1)
N [auth M]	RNA_pol_Rpb2_6,RNA_pol_Rpb2_7	e2o5iM7	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RNA_pol_Rpb2_6,RNA_pol_Rpb2_7	ECOD (v294.1)
N [auth M]	Lyase_aromatic	e2o5iM6	A: a/b three-layered sandwiches	X: UBC-like	H: UBC-like	T: Concanavalin A-like lectins/glucanases	F: Lyase_aromatic	ECOD (v294.1)
N [auth M]	Pectate_lyase_2	e2o5iM8	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Pectate_lyase_2	ECOD (v294.1)
I [auth C]	RNA_pol_Rpb2_2	e2o5iC4	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RNA_pol_Rpb2_2	ECOD (v294.1)
I [auth C]	RNA_pol_Rpb2_6,RNA_pol_Rpb2_7	e2o5iC7	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RNA_pol_Rpb2_6,RNA_pol_Rpb2_7	ECOD (v294.1)
I [auth C]	Lyase_aromatic	e2o5iC6	A: a/b three-layered sandwiches	X: UBC-like	H: UBC-like	T: Concanavalin A-like lectins/glucanases	F: Lyase_aromatic	ECOD (v294.1)
I [auth C]	Pectate_lyase_2	e2o5iC8	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Pectate_lyase_2	ECOD (v294.1)
M [auth L]	CBS	e2o5iL1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: CBS	ECOD (v294.1)
L [auth K]	CBS	e2o5iK1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: CBS	ECOD (v294.1)
H [auth B]	CBS	e2o5iB1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: CBS	ECOD (v294.1)
G [auth A]	CBS	e2o5iA1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: CBS	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
K [auth E], P [auth O]	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
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
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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
K [auth E], P [auth O]	DNA-directed RNA polymerase omega chain	DNA binding binding nucleic acid binding DNA-directed 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	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 metabolic process cellular process macromolecule metabolic process	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 DNA-directed 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 cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding DNA-directed 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 transition metal ion binding zinc 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 biosynthetic process metabolic process cellular process macromolecule metabolic process	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 DNA-directed 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 ribonucleoside binding nucleoside binding DNA binding binding nucleic acid binding DNA-directed 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 ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative 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 biosynthetic process metabolic process cellular process macromolecule metabolic process	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
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 DNA-directed 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	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 metabolic process cellular process macromolecule metabolic process	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 [auth I], F [auth Z]	5'-D(APAPCPGPCPCPAPGPAPCPAPGPGPG)-3'	-	-	-
B [auth H], E [auth Y]	5'-R(PGPAPGPUPCPUPGPCPGPGPCPGPCPGPCPG)-3'	-	-	-
A [auth G], D [auth X]	5'-D(PCPCPCPTPGPTPCPTPGPGPCPGPTPTPCPGPCPGPCPGPCPCP*G)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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
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
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

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Crystal structure of the T. thermophilus RNA polymerase elongation complex

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

2O5I | pdb_00002o5i