Annotations: 9GDP

Cryo-EM structure of Vibrio cholerae RNA polymerase holoenzyme bound to an ompU promoter DNA fragment and 5-mer RNA

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H [auth G]	MbtH	e9gdpG1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: MbtH	ECOD (v295.2)
E [auth B]		e9gdpB1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F:	ECOD (v295.2)
D [auth A]		e9gdpA1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F:	ECOD (v295.2)
C [auth E]	V-set	e9gdpE1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: V-set	ECOD (v295.2)
B [auth D]	MbtH	e9gdpD1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: MbtH	ECOD (v295.2)
A [auth C]	RNA_pol_Rpb2_6	e9gdpC1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: RNA_pol_Rpb2_6	ECOD (v295.2)
A [auth C]	RNA_pol_Rpb2_6	e9gdpC7	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: RNA_pol_Rpb2_6	ECOD (v295.2)
A [auth C]	Carb_anhydrase	e9gdpC8	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Carb_anhydrase	ECOD (v295.2)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
J [auth L]	ompU promoter template DNA strand	-	-	-
I [auth T]	ompU promoter non-template DNA strand	-	-	-
G [auth H]	RNA 5-mer (5'-AAUAG-3')	-	-	-
F	RNA polymerase sigma factor RpoD	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
D [auth A], E [auth B], H [auth G]	DNA-directed RNA polymerase subunit alpha	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
C [auth E]	DNA-directed RNA polymerase subunit omega	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	-
B [auth D]	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 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
A [auth C]	DNA-directed RNA polymerase subunit beta	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F	IPR007627	RNA polymerase sigma-70 region 2	Domain
F	IPR007127	RNA polymerase sigma factor 70, region 1.1	Domain
F	IPR000943	RNA polymerase sigma-70	Domain
F	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
F	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
F	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
F	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
F	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
F	IPR007630	RNA polymerase sigma-70 region 4	Domain
F	IPR014284	RNA polymerase sigma-70-like domain	Domain
F	IPR007624	RNA polymerase sigma-70 region 3	Domain
F	IPR007631	RNA polymerase sigma factor 70, non-essential domain	Domain
F	IPR028630	RNA polymerase sigma factor RpoD	Family
F	IPR042189	Sigma-70 factor, region 1.1 superfamily	Homologous Superfamily
F	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family
D [auth A], E [auth B], H [auth G]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
D [auth A], E [auth B], H [auth G]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
D [auth A], E [auth B], H [auth G]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
D [auth A], E [auth B], H [auth G]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
D [auth A], E [auth B], H [auth G]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
D [auth A], E [auth B], H [auth G]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
C [auth E]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
C [auth E]	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
C [auth E]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
B [auth D]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
B [auth D]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
B [auth D]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
B [auth D]	IPR012754	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Family
B [auth D]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
B [auth D]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
B [auth D]	IPR000722	RNA polymerase, alpha subunit	Domain
B [auth D]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
B [auth D]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
B [auth D]	IPR006592	RNA polymerase, N-terminal	Domain
B [auth D]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
A [auth C]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
A [auth C]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
A [auth C]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
A [auth C]	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
A [auth C]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
A [auth C]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
A [auth C]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
A [auth C]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
A [auth C]	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
A [auth C]	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
A [auth C]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
A [auth C]	IPR007641	RNA polymerase Rpb2, domain 7	Domain

9GDP | pdb_00009gdp

Cryo-EM structure of Vibrio cholerae RNA polymerase holoenzyme bound to an ompU promoter DNA fragment and 5-mer RNA

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage