Annotations: 9GDO

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

Chains

Polymer

Molecular Function

Biological Process

Cellular Component

I [auth F]

RNA polymerase sigma factor RpoD

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

DNA-directed RNA polymerase subunit omega

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

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

C [auth G],
G [auth A],
H [auth B]

DNA-directed RNA polymerase subunit alpha

B [auth N]

ompU promoter non-template DNA strand

A [auth T]

ompU promoter template DNA strand

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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
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

9GDO | pdb_00009gdo

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

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9GDO | pdb_00009gdo

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

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

9GDO | pdb_00009gdo