9N11 | pdb_00009n11

Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1.5 state

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F [auth K]	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth T]	DNA (55-MER)	-	-	-
H [auth N]	DNA (49-MER)	-	-	-
G [auth R]	RNA (5'-R(PGPGPAPGPAPGPGPUP*A)-3')	-	-	-
F [auth K]	DNA-directed RNA polymerase subunit omega	DNA binding binding nucleic acid binding RNA polymerase binding protein binding bacterial-type RNA polymerase core enzyme binding RNA polymerase core enzyme binding enzyme 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 DNA binding binding nucleic acid binding RNA polymerase binding protein binding bacterial-type RNA polymerase core enzyme binding RNA polymerase core enzyme binding enzyme 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	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 cellular component biogenesis cellular component assembly protein-containing complex assembly 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 bacterial-type flagellum organization organelle organization 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 cell motility regulation of DNA-templated transcription elongation DNA-templated transcription elongation response to heat response to abiotic stimulus response to temperature stimulus cell aggregation biofilm formation aggregation of unicellular organisms submerged biofilm formation 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-bounded organelle transcription elongation factor complex 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-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
E [auth J]	DNA-directed RNA polymerase subunit beta'	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA 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 cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA 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 transition metal ion binding zinc ion binding	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 nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol 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
D [auth I]	DNA-directed RNA polymerase subunit beta	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 ribonucleoside binding nucleoside binding 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 ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding	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 nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	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
B [auth G], C [auth H]	DNA-directed RNA polymerase subunit alpha	DNA binding binding nucleic acid binding protein binding protein dimerization activity 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	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 nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm 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
A	Transcription-repair-coupling factor	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydrolase activity catalytic activity ATP-dependent activity, acting on DNA nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity ATP-dependent activity DNA binding damaged DNA binding nucleic acid binding	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 nucleotide-excision repair, DNA damage recognition cellular response to stimulus response to stimulus transcription-coupled nucleotide-excision repair chromosome organization DNA metabolic process cellular component organization organelle organization transcription-coupled nucleotide-excision repair, DNA damage recognition cellular response to stress nucleotide-excision repair DNA damage response response to stress cellular component organization or biogenesis DNA repair	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth K]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
F [auth K]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
F [auth K]	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
E [auth J]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
E [auth J]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
E [auth J]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
E [auth J]	IPR012754	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Family
E [auth J]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
E [auth J]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
E [auth J]	IPR000722	RNA polymerase, alpha subunit	Domain
E [auth J]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
E [auth J]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
E [auth J]	IPR006592	RNA polymerase, N-terminal	Domain
E [auth J]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
D [auth I]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
D [auth I]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
D [auth I]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
D [auth I]	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
D [auth I]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
D [auth I]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
D [auth I]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
D [auth I]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
D [auth I]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
D [auth I]	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
D [auth I]	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
D [auth I]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
D [auth I]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
B [auth G], C [auth H]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
B [auth G], C [auth H]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
B [auth G], C [auth H]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
B [auth G], C [auth H]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
B [auth G], C [auth H]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
B [auth G], C [auth H]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
A	IPR004576	Transcription-repair coupling factor	Family
A	IPR041471	UvrB, interaction domain	Domain
A	IPR036101	CarD-like/TRCF, RNAP-interacting domain superfamily	Homologous Superfamily
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A	IPR037235	TRCF-like, C-terminal D7 domain	Homologous Superfamily
A	IPR048635	Transcription-repair-coupling factor, D3 domain	Domain
A	IPR047112	ATP-dependent DNA helicase RecG/Transcription-repair-coupling factor	Family
A	IPR003711	CarD-like/TRCF, RNAP-interacting domain	Domain
A	IPR011545	DEAD/DEAH-box helicase domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR005118	Transcription-repair-coupling factor, C-terminal domain	Domain