Annotations: 9W3G

Cryo-EM structure of E. coli RNA polymerase in complex with VP1

External Resource: Annotation

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F	PF04539	Sigma-70 region 3 (Sigma70_r3)	Sigma-70 region 3	-	Family
F	PF00140	Sigma-70 factor, region 1.2 (Sigma70_r1_2)	Sigma-70 factor, region 1.2	-	Family
F	PF04542	Sigma-70 region 2 (Sigma70_r2)	Sigma-70 region 2	Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA ...	Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [1,2]. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation [1,2].	Domain
F	PF04545	Sigma-70, region 4 (Sigma70_r4)	Sigma-70, region 4	Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix fami ...	Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G	Phage protein	-	-	-
F	RNA polymerase sigma factor RpoD	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region 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 DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region 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 transcription regulator activity DNA-binding transcription factor activity sigma factor activity	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of DNA-templated transcription initiation DNA-templated transcription initiation response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus	protein-containing complex intracellular anatomical structure catalytic complex transferase complex transferase complex, transferring phosphorus-containing groups cellular anatomical structure cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex sigma factor antagonist complex transcription regulator complex
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
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	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
A, 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
F	IPR007627	RNA polymerase sigma-70 region 2	Domain
F	IPR000943	RNA polymerase sigma-70	Domain
F	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
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	IPR028630	RNA polymerase sigma factor RpoD	Family
F	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family
F	IPR007127	RNA polymerase sigma factor 70, region 1.1	Domain
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	IPR007631	RNA polymerase sigma factor 70, non-essential domain	Domain
F	IPR042189	Sigma-70 factor, region 1.1 superfamily	Homologous Superfamily
E	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
E	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
E	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
D	IPR007066	RNA polymerase Rpb1, domain 3	Domain
D	IPR007081	RNA polymerase Rpb1, domain 5	Domain
D	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
D	IPR012754	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Family
D	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
D	IPR007083	RNA polymerase Rpb1, domain 4	Domain
D	IPR000722	RNA polymerase, alpha subunit	Domain
D	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
D	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
D	IPR006592	RNA polymerase, N-terminal	Domain
D	IPR007080	RNA polymerase Rpb1, domain 1	Domain
C	IPR007642	RNA polymerase Rpb2, domain 2	Domain
C	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
C	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
C	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
C	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
C	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
C	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
C	IPR007645	RNA polymerase Rpb2, domain 3	Domain
C	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
C	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
C	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
C	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
C	IPR007641	RNA polymerase Rpb2, domain 7	Domain
A, B	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
A, B	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
A, B	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
A, B	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
A, B	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
A, B	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9W3G | pdb_00009w3g

Cryo-EM structure of E. coli RNA polymerase in complex with VP1

External Resource: Annotation

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage