8D5V | pdb_00008d5v

WhiB6 bound to the SigmaAr4-RNAP Beta flap tip chimera

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	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Polyketide_cyc2	e8d5vD1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v294.1)
B		e8d5vB1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (v294.1)
C	Polyketide_cyc2	e8d5vC1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Polyketide_cyc2	ECOD (v294.1)
A	TRPM2	e8d5vA01	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: TRPM2	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	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
A, C	PF02467	Transcription factor WhiB (Whib)	Transcription factor WhiB	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta	DNA binding binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA 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 binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA 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 ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding	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 response to acid chemical response to stimulus response to chemical response to oxygen-containing compound response to abiotic stimulus response to water DNA-templated transcription initiation response to antibiotic	protein-containing complex sigma factor antagonist complex transcription regulator complex cell periphery cellular anatomical structure plasma membrane membrane external encapsulating structure extracellular region cell wall peptidoglycan-based cell wall intracellular anatomical structure cytoplasm cytosol protein-containing complex sigma factor antagonist complex transcription regulator complex cell periphery cellular anatomical structure plasma membrane membrane external encapsulating structure extracellular region cell wall peptidoglycan-based cell wall intracellular anatomical structure cytoplasm cytosol transferase complex, transferring phosphorus-containing groups catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
A, C	Probable transcriptional regulator WhiB6	DNA binding binding nucleic acid binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding dinitrosyl-iron complex binding cation binding ion binding metal ion binding	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	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR007627	RNA polymerase sigma-70 region 2	Domain
B, D	IPR000943	RNA polymerase sigma-70	Domain
B, D	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
B, D	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
B, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B, D	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
B, D	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
B, D	IPR007630	RNA polymerase sigma-70 region 4	Domain
B, D	IPR014284	RNA polymerase sigma-70-like domain	Domain
B, D	IPR007624	RNA polymerase sigma-70 region 3	Domain
B, D	IPR028630	RNA polymerase sigma factor RpoD	Family
B, D	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family
B, D	IPR007642	RNA polymerase Rpb2, domain 2	Domain
B, D	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
B, D	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
B, D	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
B, D	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
B, D	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
B, D	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
B, D	IPR007645	RNA polymerase Rpb2, domain 3	Domain
B, D	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
B, D	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
B, D	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
B, D	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
B, D	IPR007641	RNA polymerase Rpb2, domain 7	Domain
A, C	IPR034768	WhiB-like iron-sulfur binding domain	Domain
A, C	IPR003482	Transcription factor WhiB	Family