9GDS | pdb_00009gds

Cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with ToxR and TcpP transcription factors and a toxT promoter DNA fragment

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
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)
L [auth I]	e9gdsI1	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)
I [auth B]	e9gdsB1	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)
K [auth G]	e9gdsG1	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 A]	e9gdsA1	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 E]	e9gdsE1	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)
F [auth D]	e9gdsD1	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)
E [auth C]	e9gdsC1	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: RNA_pol_Rpb2_6	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
L [auth I]	PF00486	Transcriptional regulatory protein, C terminal (Trans_reg_C)	Transcriptional regulatory protein, C terminal		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
L [auth I]	Cholera toxin transcriptional activator	DNA binding binding nucleic acid binding molecular transducer activity phosphorelay response regulator activity	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	cell periphery cellular anatomical structure plasma membrane membrane
J [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
H [auth A], I [auth B], K [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 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 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
F [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
E [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
D [auth T]	toxT promoter template DNA strand	-	-	-
C [auth N]	toxT promoter non-template DNA strand	-	-	-
A [auth H], B [auth K]	Toxin co-regulated pilus biosynthesis protein P	DNA binding binding nucleic acid binding	cellular response to stimulus regulation of biological process phosphorelay signal transduction system regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication cellular process signal transduction RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process cellular response to stimulus regulation of biological process phosphorelay signal transduction system regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication cellular process signal transduction RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
L [auth I]	IPR001867	OmpR/PhoB-type DNA-binding domain	Domain
L [auth I]	IPR016032	Signal transduction response regulator, C-terminal effector	Homologous Superfamily
L [auth I]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
J [auth F]	IPR007627	RNA polymerase sigma-70 region 2	Domain
J [auth F]	IPR007127	RNA polymerase sigma factor 70, region 1.1	Domain
J [auth F]	IPR000943	RNA polymerase sigma-70	Domain
J [auth F]	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
J [auth F]	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
J [auth F]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
J [auth F]	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
J [auth F]	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
J [auth F]	IPR007630	RNA polymerase sigma-70 region 4	Domain
J [auth F]	IPR014284	RNA polymerase sigma-70-like domain	Domain
J [auth F]	IPR007624	RNA polymerase sigma-70 region 3	Domain
J [auth F]	IPR007631	RNA polymerase sigma factor 70, non-essential domain	Domain
J [auth F]	IPR028630	RNA polymerase sigma factor RpoD	Family
J [auth F]	IPR042189	Sigma-70 factor, region 1.1 superfamily	Homologous Superfamily
J [auth F]	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family
H [auth A], I [auth B], K [auth G]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
H [auth A], I [auth B], K [auth G]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
H [auth A], I [auth B], K [auth G]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
H [auth A], I [auth B], K [auth G]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
H [auth A], I [auth B], K [auth G]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
H [auth A], I [auth B], K [auth G]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
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]	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]	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
A [auth H], B [auth K]	IPR001867	OmpR/PhoB-type DNA-binding domain	Domain
A [auth H], B [auth K]	IPR016032	Signal transduction response regulator, C-terminal effector	Homologous Superfamily
A [auth H], B [auth K]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily