6PFV

Structure of S. venezuelae RisG-WhiG-c-di-GMP complex: orthorhombic crystal form

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
B [auth A]	Sigma70_r3	e6pfvA2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r3	ECOD (1.6)
B [auth A]	Sigma70_r4_2	e6pfvA3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4_2	ECOD (1.6)
B [auth A]	Sigma70_r2_2	e6pfvA1	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)
D	Sigma70_r3	e6pfvD2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r3	ECOD (1.6)
D	Sigma70_r4_2	e6pfvD3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4_2	ECOD (1.6)
D	Sigma70_r2_2	e6pfvD1	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)
F [auth G]	Sigma70_r3	e6pfvG3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r3	ECOD (1.6)
F [auth G]	Sigma70_r4_2	e6pfvG1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4_2	ECOD (1.6)
F [auth G]	Sigma70_r2_2	e6pfvG2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A], D, F [auth G]	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
B [auth A], D, F [auth G]	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 [auth T], C [auth B], E	AmfC protein	-	-	-
B [auth A], D, F [auth G]	RNA polymerase sigma factor	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' 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 transcription regulator activity DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' 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 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 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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth T], C [auth B], E	IPR049575	Anti-sigma factor RsiG/AmfC-like	Family
B [auth A], D, F [auth G]	IPR007627	RNA polymerase sigma-70 region 2	Domain
B [auth A], D, F [auth G]	IPR000943	RNA polymerase sigma-70	Domain
B [auth A], D, F [auth G]	IPR007624	RNA polymerase sigma-70 region 3	Domain
B [auth A], D, F [auth G]	IPR012845	RNA polymerase sigma factor, FliA/WhiG	Family
B [auth A], D, F [auth G]	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
B [auth A], D, F [auth G]	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
B [auth A], D, F [auth G]	IPR014284	RNA polymerase sigma-70 like domain	Domain
B [auth A], D, F [auth G]	IPR007630	RNA polymerase sigma-70 region 4	Domain

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.