1L9Z | pdb_00001l9z

Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
H	d1l9zh_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	DNA-directed RNA polymerase alpha(2), beta, beta-prime and omega subunits	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
G [auth E]	d1l9ze_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	DNA-directed RNA polymerase alpha(2), beta, beta-prime and omega subunits	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
F [auth D]	d1l9zd_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	DNA-directed RNA polymerase alpha(2), beta, beta-prime and omega subunits	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
E [auth C]	d1l9zc_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	DNA-directed RNA polymerase alpha(2), beta, beta-prime and omega subunits	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
D [auth B]	d1l9zb_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	DNA-directed RNA polymerase alpha(2), beta, beta-prime and omega subunits	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
C [auth A]	d1l9za_	Low resolution protein structures	RNA polymerase	RNA polymerase	RNA polymerase	DNA-directed RNA polymerase alpha(2), beta, beta-prime and omega subunits	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Sigma factor domain-like	8040679	3000953	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Sigma factor domain-like	8044410	3000953	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Sigma2 domain of RNA polymerase sigma factors	8044411	3001393	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	RPB6/omega subunit-like	8034762	3000189	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8032539	3001330	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8032536	3001330	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8032536	3001330	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8034760	3001500	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8034760	3001500	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)
H	YonK	e1l9zH2	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: YonK	ECOD (v294.1)
H	CBS	e1l9zH4	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: CBS	ECOD (v294.1)
G [auth E]	Flavi_glycoprot	e1l9zE1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Flavi_glycoprot	ECOD (v294.1)
F [auth D]	EF-hand_1, EF-hand_7	e1l9zD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: EF-hand_1, EF-hand_7	ECOD (v294.1)
E [auth C]	UvrB_inter	e1l9zC1	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: UvrB_inter	ECOD (v294.1)
D [auth B]	Flavi_glycoprot	e1l9zB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Flavi_glycoprot	ECOD (v294.1)
C [auth A]	Flavi_glycoprot	e1l9zA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Flavi_glycoprot	ECOD (v294.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H	SIGMA FACTOR SIGA	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor activity	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation 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 RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation 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
G [auth E]	RNA POLYMERASE, OMEGA SUBUNIT	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
F [auth D]	RNA POLYMERASE, BETA-PRIME SUBUNIT	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
E [auth C]	RNA POLYMERASE, BETA SUBUNIT	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
C [auth A], D [auth B]	RNA POLYMERASE, ALPHA SUBUNIT	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
B [auth T]	template DNA strand	-	-	-
A [auth U]	nontemplate DNA strand	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H	IPR007627	RNA polymerase sigma-70 region 2	Domain
H	IPR000943	RNA polymerase sigma-70	Domain
H	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
H	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
H	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
H	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
H	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
H	IPR007630	RNA polymerase sigma-70 region 4	Domain
H	IPR014284	RNA polymerase sigma-70-like domain	Domain
H	IPR007624	RNA polymerase sigma-70 region 3	Domain
H	IPR028630	RNA polymerase sigma factor RpoD	Family
H	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family
G [auth E]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
G [auth E]	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
G [auth E]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
F [auth D]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
F [auth D]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
F [auth D]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
F [auth D]	IPR012754	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Family
F [auth D]	IPR048566	DNA-directed RNA polymerase subunit beta', hybrid domain	Domain
F [auth D]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
F [auth D]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
F [auth D]	IPR000722	RNA polymerase, alpha subunit	Domain
F [auth D]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
F [auth D]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
F [auth D]	IPR006592	RNA polymerase, N-terminal	Domain
F [auth D]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
E [auth C]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
E [auth C]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
E [auth C]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
E [auth C]	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
E [auth C]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
E [auth C]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
E [auth C]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
E [auth C]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
E [auth C]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
E [auth C]	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
E [auth C]	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
E [auth C]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
E [auth C]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
C [auth A], D [auth B]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
C [auth A], D [auth B]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
C [auth A], D [auth B]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
C [auth A], D [auth B]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
C [auth A], D [auth B]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily