8CWR | pdb_00008cwr

Complex structure of WhiB3 and the SigmaAr4-RNAP Beta flap tip chimera in space group R3

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	F_UNCLASSIFIED	e8cwrA1	A: alpha arrays	X: 4Fe-4S binding domain in Dna2	H: 4Fe-4S protein WhiB1 (From Topology)	T: 4Fe-4S protein WhiB1	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8cwrB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02467	Transcription factor WhiB (Whib)	Transcription factor WhiB	-	Family
B	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
A	Redox- and pH-responsive transcriptional regulator WhiB3	DNA binding binding nucleic acid binding iron-sulfur cluster binding metal cluster binding small molecule binding dinitrosyl-iron complex binding oxidoreductase activity, acting on a sulfur group of donors disulfide oxidoreductase activity oxidoreductase activity catalytic activity, acting on a protein protein-disulfide reductase activity catalytic activity protein-disulfide reductase [NAD(P)H] activity DNA binding binding nucleic acid binding iron-sulfur cluster binding metal cluster binding small molecule binding dinitrosyl-iron complex binding oxidoreductase activity, acting on a sulfur group of donors disulfide oxidoreductase activity oxidoreductase activity catalytic activity, acting on a protein protein-disulfide reductase activity catalytic activity protein-disulfide reductase [NAD(P)H] activity oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor 4 iron, 4 sulfur cluster binding cation binding ion binding metal ion binding	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 biological process involved in interspecies interaction between organisms response to host redox environment response to stimulus response to other organism response to external stimulus response to host response to external biotic stimulus response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction regulation of lipid metabolic process lipid metabolic process cellular component biogenesis peptidoglycan-based cell wall biogenesis cell wall biogenesis cell wall organization or biogenesis Actinobacterium-type cell wall biogenesis cellular component organization or biogenesis cell redox homeostasis cellular homeostasis homeostatic process	cell periphery cellular anatomical structure external encapsulating structure cell wall peptidoglycan-based cell wall intracellular anatomical structure cytoplasm
B	RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor 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 DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor 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 ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding	response to acid chemical response to stimulus response to chemical response to oxygen-containing compound response to abiotic stimulus response to water 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 response to acid chemical response to stimulus response to chemical response to oxygen-containing compound response to abiotic stimulus response to water 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 response to antibiotic	cell periphery cellular anatomical structure plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall intracellular anatomical structure cytoplasm cytosol transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex cell periphery cellular anatomical structure plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall 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

InterPro: Protein Family Classification InterPro Database Homepage

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