9GDO | pdb_00009gdo

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

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth C]	e9gdoC1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: Galactose-binding domain-like	T:	F:	ECOD (20:10:01)
D [auth C]	e9gdoC4	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: Galactose-binding domain-like	T: PC_rep, HEAT_2, RPN2_C	F:	ECOD (20:10:01)
F [auth E]	e9gdoE1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: N-terminal domain of the delta subunit of the F1F0-ATP synthase	T: Carb_anhydrase	F:	ECOD (20:10:01)
E [auth D]	e9gdoD1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: N-terminal domain of the delta subunit of the F1F0-ATP synthase	T: MbtH	F:	ECOD (20:10:01)
C [auth G]	e9gdoG1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: N-terminal domain of the delta subunit of the F1F0-ATP synthase	T: MbtH	F:	ECOD (20:10:01)
H [auth B]	e9gdoB1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: N-terminal domain of the delta subunit of the F1F0-ATP synthase	T:	F:	ECOD (20:10:01)
G [auth A]	e9gdoA1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: Galactose-binding domain-like	T:	F:	ECOD (20:10:01)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth T]	ompU promoter template DNA strand	-	-	-
B [auth N]	ompU promoter non-template DNA strand	-	-	-
D [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	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 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
F [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	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 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 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 G], G [auth A], H [auth B]	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 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

InterPro: Protein Family Classification InterPro Database Homepage

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