2P7V

Crystal structure of the Escherichia coli regulator of sigma 70, Rsd, in complex with sigma 70 domain 4

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2p7vb_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma4 domain	Sigma70 (SigA, RpoD)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Rsd/AlgQ-like	8045786	4004685	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Rsd/AlgQ-like	8092079	3002560	SCOP2 (2022-06-29)
B	SCOP2 Family	Sigma4 domain	8023072	4003503	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Sigma factor domain-like	8035452	3000953	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Rsd_AlgQ	e2p7vA1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ (From Topology)	T: Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ	F: Rsd_AlgQ	ECOD (1.6)
B	Sigma70_r4	e2p7vB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.1370	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Regulator of RNA polymerase sigma(70) subunit, domain 4	CATH (4.3.0)
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 (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04353	Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ (Rsd_AlgQ)	Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ	-	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	Regulator of sigma D	RNA polymerase binding protein binding binding bacterial-type RNA polymerase core enzyme binding RNA polymerase core enzyme binding enzyme binding sigma factor antagonist activity transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process catabolic process positive regulation of nucleotide metabolic process positive regulation of biological process organophosphate catabolic process positive regulation of cellular metabolic process nucleoside phosphate catabolic process positive regulation of phosphate metabolic process positive regulation of metabolic process positive regulation of nucleotide catabolic process regulation of small molecule metabolic process nucleobase-containing small molecule metabolic process regulation of nucleotide metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleotide catabolic process positive regulation of cellular process nucleoside phosphate metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of phosphorus metabolic process regulation of catabolic process nucleotide metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process positive regulation of catabolic process organophosphate metabolic process regulation of nucleotide catabolic process regulation of phosphorus metabolic process positive regulation of small molecule metabolic process organic substance catabolic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress stringent response response to starvation cellular response to starvation	protein-containing complex sigma factor antagonist complex transcription regulator complex intracellular anatomical structure cytoplasm cellular anatomical entity
B	RNA polymerase sigma factor rpoD	DNA binding binding organic cyclic compound binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor activity cation binding ion binding metal ion binding small molecule binding	cellular biosynthetic process cellular metabolic 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process cellular biosynthetic process cellular metabolic 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023785	Regulator of RNA polymerase sigma(70) subunit, Rsd	Family
A	IPR038309	Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ superfamily	Homologous Superfamily
A	IPR007448	Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ	Family
B	IPR007627	RNA polymerase sigma-70 region 2	Domain
B	IPR007127	RNA polymerase sigma factor 70, region 1.1	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	IPR014284	RNA polymerase sigma-70 like domain	Domain
B	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
B	IPR007630	RNA polymerase sigma-70 region 4	Domain
B	IPR007624	RNA polymerase sigma-70 region 3	Domain
B	IPR007631	RNA polymerase sigma factor 70, non-essential domain	Domain
B	IPR028630	RNA polymerase sigma factor RpoD	Family
B	IPR042189	Sigma-70 factor, region 1.1 superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.