4KI2 | pdb_00004ki2

Crystallographic analysis of an RNA-polymerase sigma-subunit fragment complexed with -10 promoter element ssDNA

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)
F [auth B]	SCOP2B Superfamily	Sigma factor domain-like	8044410	3000953	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Sigma2 domain of RNA polymerase sigma factors	8044411	3001393	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	Sigma2 domain of RNA polymerase sigma factors	8044411	3001393	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth B]	Sigma70_r3	e4ki2B1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r3	ECOD (1.6)
F [auth B]	Sigma70_r2_2	e4ki2B2	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)
E [auth A]	Sigma70_r2_2	e4ki2A1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth B]	1.20.120.1810	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
F [auth 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)
E [auth A]	1.20.120.1810	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth B]	PF04539	Sigma-70 region 3 (Sigma70_r3)	Sigma-70 region 3	-	Family
E [auth A], F [auth B]	PF00140	Sigma-70 factor, region 1.2 (Sigma70_r1_2)	Sigma-70 factor, region 1.2	-	Family
E [auth A], F [auth B]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth A], F [auth B]	RNA polymerase sigma factor	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor activity	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 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	cellular anatomical structure intracellular anatomical structure cytoplasm
A [auth D], B [auth E], C [auth F], D [auth G]	DNA (5'-D(TPGPTPAPCPAPAPTPGPGP*G)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B]	IPR007627	RNA polymerase sigma-70 region 2	Domain
E [auth A], F [auth B]	IPR000943	RNA polymerase sigma-70	Domain
E [auth A], F [auth B]	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
E [auth A], F [auth B]	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
E [auth A], F [auth B]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
E [auth A], F [auth B]	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
E [auth A], F [auth B]	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
E [auth A], F [auth B]	IPR007630	RNA polymerase sigma-70 region 4	Domain
E [auth A], F [auth B]	IPR014284	RNA polymerase sigma-70-like domain	Domain
E [auth A], F [auth B]	IPR007624	RNA polymerase sigma-70 region 3	Domain
E [auth A], F [auth B]	IPR028630	RNA polymerase sigma factor RpoD	Family
E [auth A], F [auth B]	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.