6ONU | pdb_00006onu

Complex structure of WhiB1 and region 4 of SigA in P21 space group.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d6onub_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
D	d6onud_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
F	d6onuf_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
H	d6onuh_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	UNK_F_TYPE	e6onuA1	A: alpha arrays	X: 4Fe-4S binding domain in Dna2	H: 4Fe-4S protein WhiB1 (From Topology)	T: 4Fe-4S protein WhiB1	F: UNK_F_TYPE	ECOD (1.6)
C	UNK_F_TYPE	e6onuC1	A: alpha arrays	X: 4Fe-4S binding domain in Dna2	H: 4Fe-4S protein WhiB1 (From Topology)	T: 4Fe-4S protein WhiB1	F: UNK_F_TYPE	ECOD (1.6)
E	UNK_F_TYPE	e6onuE1	A: alpha arrays	X: 4Fe-4S binding domain in Dna2	H: 4Fe-4S protein WhiB1 (From Topology)	T: 4Fe-4S protein WhiB1	F: UNK_F_TYPE	ECOD (1.6)
G	UNK_F_TYPE	e6onuG1	A: alpha arrays	X: 4Fe-4S binding domain in Dna2	H: 4Fe-4S protein WhiB1 (From Topology)	T: 4Fe-4S protein WhiB1	F: UNK_F_TYPE	ECOD (1.6)
B	Sigma70_r4	e6onuB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4	ECOD (1.6)
D	Sigma70_r4	e6onuD1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4	ECOD (1.6)
F	Sigma70_r4	e6onuF1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4	ECOD (1.6)
H	Sigma70_r4	e6onuH1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF02467	Transcription factor WhiB (Whib)	Transcription factor WhiB	-	Family
B, D, F, H	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, C, E, G	Transcriptional regulator WhiB1	DNA binding binding nucleic acid binding protein-disulfide reductase [NAD(P)H] activity oxidoreductase activity, acting on a sulfur group of donors oxidoreductase activity disulfide oxidoreductase activity catalytic activity, acting on a protein protein-disulfide reductase activity catalytic activity oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding DNA binding binding nucleic acid binding protein-disulfide reductase [NAD(P)H] activity oxidoreductase activity, acting on a sulfur group of donors oxidoreductase activity disulfide oxidoreductase activity catalytic activity, acting on a protein protein-disulfide reductase activity catalytic activity oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor 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 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 cell redox homeostasis cellular homeostasis homeostatic process response to stimulus response to chemical response to nitric oxide response to oxygen-containing compound response to nitrogen compound	cellular anatomical structure intracellular anatomical structure cytoplasm
B, D, F, H	RNA polymerase sigma factor SigA	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor activity	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	cell periphery cellular anatomical structure plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR034768	WhiB-like iron-sulfur binding domain	Domain
A, C, E, G	IPR003482	Transcription factor WhiB	Family
B, D, F, H	IPR007627	RNA polymerase sigma-70 region 2	Domain
B, D, F, H	IPR000943	RNA polymerase sigma-70	Domain
B, D, F, H	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
B, D, F, H	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
B, D, F, H	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B, D, F, H	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
B, D, F, H	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
B, D, F, H	IPR007630	RNA polymerase sigma-70 region 4	Domain
B, D, F, H	IPR014284	RNA polymerase sigma-70-like domain	Domain
B, D, F, H	IPR007624	RNA polymerase sigma-70 region 3	Domain
B, D, F, H	IPR028630	RNA polymerase sigma factor RpoD	Family
B, D, F, H	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family

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.