5YIX

Caulobacter crescentus GcrA sigma-interacting domain (SID) in complex with domain 2 of sigma 70

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Sigma2 domain of RNA polymerase sigma factors	8069326	4003741	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sigma2 domain of RNA polymerase sigma factors	8069327	3001393	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	Sigma70_r2_2	e5yixA1	A: alpha complex topology	X: Sigma2 domain-like	H: Sigma2 domain of RNA polymerase sigma factors (From Topology)	T: Sigma2 domain of RNA polymerase sigma factors	F: Sigma70_r2_2	ECOD (1.6)
B	UNK_F_TYPE	e5yixB1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: Primase zinc finger (From Topology)	T: Primase zinc finger	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.601.10	Mainly Alpha	Orthogonal Bundle	RNA Polymerase Primary Sigma Factor	RNA Polymerase Primary Sigma Factor	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00140	Sigma-70 factor, region 1.2 (Sigma70_r1_2)	Sigma-70 factor, region 1.2	-	Family
A	PF04542	Sigma-70 region 2 (Sigma70_r2)	Sigma-70 region 2	Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA ...	Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [1,2]. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation [1,2].	Domain
A	PF04546	Sigma-70, non-essential region (Sigma70_ner)	Sigma-70, non-essential region	The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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	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 nucleic acid biosynthetic process biosynthetic 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 nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity
B	Cell cycle regulatory protein GcrA	cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007627	RNA polymerase sigma-70 region 2	Domain
A	IPR007127	RNA polymerase sigma factor 70, region 1.1	Domain
A	IPR000943	RNA polymerase sigma-70	Domain
A	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
A	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
A	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
A	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
A	IPR007630	RNA polymerase sigma-70 region 4	Domain
A	IPR014284	RNA polymerase sigma-70-like domain	Domain
A	IPR007624	RNA polymerase sigma-70 region 3	Domain
A	IPR007631	RNA polymerase sigma factor 70, non-essential domain	Domain
A	IPR028630	RNA polymerase sigma factor RpoD	Family
A	IPR042189	Sigma-70 factor, region 1.1 superfamily	Homologous Superfamily
A	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family
B	IPR011681	GcrA cell cycle regulator	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 R01GM133198.