3VEP | pdb_00003vep

Crystal structure of SigD4 in complex with its negative regulator RsdA

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 [auth X]	SCOP2B Superfamily	RsdA N-terminal domain-like	8092847	3002632	SCOP2B (2022-06-29)
G [auth J]	SCOP2B Superfamily	RsdA N-terminal domain-like	8092847	3002632	SCOP2B (2022-06-29)
E [auth G]	SCOP2 Family	RsdA N-terminal domain-like	8046093	4004872	SCOP2 (2022-06-29)
E [auth G]	SCOP2 Superfamily	RsdA N-terminal domain-like	8092847	3002632	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	RsdA N-terminal domain-like	8092847	3002632	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 E]	Sigma70_r4_2	e3vepE2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4_2	ECOD (1.6)
H	Sigma70_r4_2	e3vepH1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4_2	ECOD (1.6)
D [auth A]	Sigma70_r4_2	e3vepA2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4_2	ECOD (1.6)
B [auth D]	Sigma70_r4_2	e3vepD3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4_2	ECOD (1.6)
A [auth X]	RsdA_SigD_bd	e3vepX1	A: alpha arrays	X: Negative regulator RsdA N-terminal domain (From Topology)	H: Negative regulator RsdA N-terminal domain (From Topology)	T: Negative regulator RsdA N-terminal domain	F: RsdA_SigD_bd	ECOD (1.6)
G [auth J]	RsdA_SigD_bd	e3vepJ1	A: alpha arrays	X: Negative regulator RsdA N-terminal domain (From Topology)	H: Negative regulator RsdA N-terminal domain (From Topology)	T: Negative regulator RsdA N-terminal domain	F: RsdA_SigD_bd	ECOD (1.6)
E [auth G]	RsdA_SigD_bd	e3vepG1	A: alpha arrays	X: Negative regulator RsdA N-terminal domain (From Topology)	H: Negative regulator RsdA N-terminal domain (From Topology)	T: Negative regulator RsdA N-terminal domain	F: RsdA_SigD_bd	ECOD (1.6)
C	RsdA_SigD_bd	e3vepC1	A: alpha arrays	X: Negative regulator RsdA N-terminal domain (From Topology)	H: Negative regulator RsdA N-terminal domain (From Topology)	T: Negative regulator RsdA N-terminal domain	F: RsdA_SigD_bd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth E]	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)
H	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)
D [auth A]	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)
B [auth D]	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)
A [auth X]	6.10.250.1300	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
G [auth J]	6.10.250.1300	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
E [auth G]	6.10.250.1300	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C	6.10.250.1300	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth D], D [auth A], F [auth E], H	PF08281	Sigma-70, region 4 (Sigma70_r4_2)	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].	Domain
A [auth X], C, E [auth G], G [auth J]	PF16751	Anti-sigma-D factor RsdA to sigma factor binding region (RsdA_SigD_bd)	Anti-sigma-D factor RsdA to sigma factor binding region	RsdA_SigD_bd is a domain at the N-terminus of anti-sigma-D factor RsdA proteins. It binds to the -35 promoter binding domain of sigma-D. The complex formed regulates the transcriptional expression of the bacterium [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth D], D [auth A], F [auth E], H	Probable RNA polymerase sigma-D factor	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor activity	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological 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 cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process DNA-templated transcription initiation response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus	-
A [auth X], C, E [auth G], G [auth J]	Uncharacterized protein Rv3413c/MT3522	-	-	cell periphery cellular anatomical structure plasma membrane membrane extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D], D [auth A], F [auth E], H	IPR007627	RNA polymerase sigma-70 region 2	Domain
B [auth D], D [auth A], F [auth E], H	IPR039425	RNA polymerase sigma-70-like	Family
B [auth D], D [auth A], F [auth E], H	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
B [auth D], D [auth A], F [auth E], H	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
B [auth D], D [auth A], F [auth E], H	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B [auth D], D [auth A], F [auth E], H	IPR000838	RNA polymerase sigma factor 70, ECF, conserved site	Conserved Site
B [auth D], D [auth A], F [auth E], H	IPR014284	RNA polymerase sigma-70-like domain	Domain
B [auth D], D [auth A], F [auth E], H	IPR013249	RNA polymerase sigma factor 70, region 4 type 2	Domain
A [auth X], C, E [auth G], G [auth J]	IPR031928	Anti-sigma-D factor RsdA, sigma factor binding region	Domain

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.