6IDO

Crystal structure of Klebsiella pneumoniae sigma4 of sigmaS fusing with the RNA polymerase beta-flap-tip-helix in complex with -35 element DNA

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)
A	RNA_pol_Rpb2_6_2nd,Sigma70_r4	e6idoA1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: RNA_pol_Rpb2_6_2nd,Sigma70_r4	ECOD (1.6)
D [auth B]	RNA_pol_Rpb2_6_2nd,Sigma70_r4	e6idoB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: RNA_pol_Rpb2_6_2nd,Sigma70_r4	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth B]	PF00562	RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)	RNA polymerase Rpb2, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).	Domain
A, D [auth B]	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, D [auth B]	RNA polymerase sigma factor RpoS,RNA polymerase beta-flap-tip-helix	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 ribonucleoside binding 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 ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding RNA polymerase binding protein binding bacterial-type RNA polymerase core enzyme binding RNA polymerase core enzyme binding enzyme 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 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 cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process 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 regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of gene expression negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process regulation of DNA-templated transcription initiation DNA-templated transcription initiation	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex sigma factor antagonist complex transcription regulator complex intracellular anatomical structure cellular anatomical entity cytosolic DNA-directed RNA polymerase complex cytoplasm cytosol
B [auth C], E	DNA (5'-D(PGPAPTPTPTPGPTPCPAPAPGPTPGPGP*C)-3')	-	-	-
C [auth D], F	DNA (5'-D(PCPCPAPCPTPTPGPAPCPAPAPAPTPCP*G)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
A, D [auth B]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
A, D [auth B]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
A, D [auth B]	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
A, D [auth B]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
A, D [auth B]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
A, D [auth B]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
A, D [auth B]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
A, D [auth B]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
A, D [auth B]	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
A, D [auth B]	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
A, D [auth B]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
A, D [auth B]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
A, D [auth B]	IPR007627	RNA polymerase sigma-70 region 2	Domain
A, D [auth B]	IPR000943	RNA polymerase sigma-70	Domain
A, D [auth B]	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
A, D [auth B]	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
A, D [auth B]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, D [auth B]	IPR014284	RNA polymerase sigma-70 like domain	Domain
A, D [auth B]	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
A, D [auth B]	IPR007630	RNA polymerase sigma-70 region 4	Domain
A, D [auth B]	IPR007624	RNA polymerase sigma-70 region 3	Domain
A, D [auth B]	IPR012761	RNA polymerase sigma factor RpoS	Family

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.

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6IDO

Crystal structure of Klebsiella pneumoniae sigma4 of sigmaS fusing with the RNA polymerase beta-flap-tip-helix in complex with -35 element DNA

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage