3N97 | pdb_00003n97

RNA polymerase alpha C-terminal domain (E. coli) and sigma region 4 (T. aq. mutant) bound to (UP,-35 element) DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B [auth D]	SCOP2B Superfamily	Sigma factor domain-like	8040679	3000953	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sigma factor domain-like	8040679	3000953	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	C-terminal domain of RNA polymerase alpha subunit	8042964	3000519	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	C-terminal domain of RNA polymerase alpha subunit	8042964	3000519	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)
B [auth D]	Flavin_Reduct	e3n97D1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (v294.1)
A	Asp_Glu_race	e3n97A1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Asp_Glu_race	ECOD (v294.1)
D [auth C]	Flavin_Reduct	e3n97C1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (v294.1)
C [auth B]	Flavin_Reduct	e3n97B1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	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 C]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
C [auth B]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth D]	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
F [auth N]	DNA (5'-D(CPCPAPTPGPTPCPAPAPGPTPAPCPTPTPTPTPTPTPCP*C)-3')	-	-	-
E [auth M]	DNA (5'-D(TPGPGPAPAPAPAPAPAPGPTPAPCPTPTPGPAPCPAPTPGPG)-3')	-	-	-
C [auth B], D [auth C]	DNA-directed RNA polymerase subunit alpha	DNA binding binding nucleic acid binding DNA-directed 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 protein binding protein dimerization activity	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization negative regulation of metabolic process primary metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination positive regulation of biological process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression negative regulation of biosynthetic process cellular process regulation of DNA-templated transcription initiation DNA-templated transcription initiation cellular response to stimulus cellular response to stress response to stimulus response to stress cellular response to cell envelope stress organelle assembly cell projection organization bacterial-type flagellum assembly membraneless organelle assembly cellular component biogenesis bacterial-type flagellum organization organelle organization cellular component assembly cell projection assembly nitrate assimilation nitrogen cycle metabolic process oxoacid metabolic process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process regulation of DNA-templated transcription elongation DNA-templated transcription elongation cell aggregation biofilm formation aggregation of unicellular organisms submerged biofilm formation cell motility response to heat response to abiotic stimulus response to temperature stimulus bacterial-type flagellum-dependent cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility	protein-containing complex intracellular anatomical structure catalytic complex transferase complex transferase complex, transferring phosphorus-containing groups cellular anatomical structure cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex transferase complex transferase complex, transferring phosphorus-containing groups cellular anatomical structure cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane membrane-bounded organelle transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth D]	IPR007627	RNA polymerase sigma-70 region 2	Domain
A, B [auth D]	IPR000943	RNA polymerase sigma-70	Domain
A, B [auth D]	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
A, B [auth D]	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
A, B [auth D]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B [auth D]	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
A, B [auth D]	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
A, B [auth D]	IPR007630	RNA polymerase sigma-70 region 4	Domain
A, B [auth D]	IPR014284	RNA polymerase sigma-70-like domain	Domain
A, B [auth D]	IPR007624	RNA polymerase sigma-70 region 3	Domain
A, B [auth D]	IPR028630	RNA polymerase sigma factor RpoD	Family
A, B [auth D]	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family
C [auth B], D [auth C]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
C [auth B], D [auth C]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
C [auth B], D [auth C]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
C [auth B], D [auth C]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
C [auth B], D [auth C]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
C [auth B], D [auth C]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.