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	Sigma70_r3	e1l9zH3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r3	ECOD (1.6)
H	Sigma70_r4	e1l9zH4	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4	ECOD (1.6)
H	Sigma70_r2_2	e1l9zH2	A: alpha complex topology	X: Sigma2 domain-like	H: Sigma2 domain of RNA polymerase sigma factors (From Topology)	T: Sigma2 domain of RNA polymerase sigma factors	F: Sigma70_r2_2	ECOD (1.6)
G [auth E]	RNA_pol_Rpb6	e1l9zE1	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)
F [auth D]	RNA_pol_Rpb1_2	e1l9zD3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
F [auth D]	PRK00566_1st	e1l9zD1	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)
F [auth D]	PRK00566_2nd	e1l9zD2	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)
F [auth D]	RNA_pol_Rpb1_5_2nd	e1l9zD5	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)
F [auth D]	RNA_pol_Rpb1_1	e1l9zD8	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)
F [auth D]	RNA_pol_Rpb1_5_3rd	e1l9zD6	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)
F [auth D]	RNA_pol_Rpb1_4	e1l9zD7	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)
F [auth D]	RNA_pol_Rpb1_3	e1l9zD4	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 [auth C]	RNA_pol_Rpb2_6_3rd_3	e1l9zC3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_3	ECOD (1.6)
E [auth C]	RNA_pol_Rpb2_6_1st_1	e1l9zC2	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)
E [auth C]	RNA_pol_Rpb2_6_2nd	e1l9zC4	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)
E [auth C]	RNA_pol_Rpb2_3	e1l9zC6	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)
E [auth C]	RNA_pol_Rpb2_1	e1l9zC5	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)
E [auth C]	RNA_pol_Rpb2_45	e1l9zC1	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)
E [auth C]	RNA_pol_Rpb2_7	e1l9zC7	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 [auth B]	RNA_pol_L	e1l9zB1	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)
D [auth B]	RNA_pol_A_bac	e1l9zB2	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 [auth A]	RNA_pol_L	e1l9zA1	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)
C [auth A]	RNA_pol_A_bac	e1l9zA2	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)

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