9K17 | pdb_00009k17

A cryo-EM structure of B. oleracea RNA polymerase V in complex with 6U sacffold at 3.04 Angstrom

External Resource: Annotation

Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth T]	DNA (34-MER)	-	-	-
B [auth N]	DNA (34-MER)	-	-	-
C [auth P]	RNA (5'-R(UPAPUPAPUPGPCPAPGPAPAPAPGPCPUPUPUPUPUPU)-3')	-	-	-
D [auth A]	DNA-directed RNA polymerase V largest subunit	-	-	-
E [auth C]	DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein	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	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 transcription by RNA polymerase II biosynthetic process metabolic process cellular 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 nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure RNA polymerase V complex organelle RNA polymerase complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure RNA polymerase V complex organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase IV complex RNA polymerase II, holoenzyme membrane-enclosed lumen intracellular organelle lumen nucleoplasm RNA polymerase II, core complex nuclear DNA-directed RNA polymerase complex organelle lumen nuclear lumen
F	DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein	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	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 transcription by RNA polymerase I metabolic process cellular 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 nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I metabolic process cellular process macromolecule metabolic process transcription by RNA polymerase II tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription by RNA polymerase III	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure RNA polymerase V complex organelle RNA polymerase complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure RNA polymerase V complex organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase I complex membrane-enclosed lumen intracellular organelle lumen membraneless organelle intracellular membraneless organelle nucleolus organelle lumen nuclear lumen RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex nuclear DNA-directed RNA polymerase complex RNA polymerase III complex
G [auth J]	DNA-directed RNA polymerase II, IV and V subunit 10	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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 DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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	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 transcription by RNA polymerase I metabolic process cellular 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 nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I metabolic process cellular process macromolecule metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription by RNA polymerase III transcription by RNA polymerase II	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus transferase complex, transferring phosphorus-containing groups organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase III complex RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex nuclear DNA-directed RNA polymerase complex
H [auth K]	DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein	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 transcription by RNA polymerase II biosynthetic process metabolic process cellular 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 nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
I [auth L]	DNA-directed RNA polymerase II, IV and V subunit 12	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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 DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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	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	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus transferase complex, transferring phosphorus-containing groups organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase III complex RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex nuclear DNA-directed RNA polymerase complex
J [auth H]	DNA-directed RNA polymerase II, IV and V subunit 8	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	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure RNA polymerase V complex organelle RNA polymerase complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure RNA polymerase V complex organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase I complex membrane-enclosed lumen intracellular organelle lumen membraneless organelle intracellular membraneless organelle nucleolus organelle lumen nuclear lumen RNA polymerase III complex RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex nuclear DNA-directed RNA polymerase complex
K [auth I]	DNA-directed RNA polymerase subunit	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 cation binding transition metal ion binding zinc ion 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 cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II maintenance of transcriptional fidelity during transcription elongation DNA-templated transcription elongation maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II cellular response to stimulus response to stimulus transcription-coupled nucleotide-excision repair DNA metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress DNA repair	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex catalytic complex nuclear protein-containing complex transferase complex transferase complex, transferring phosphorus-containing groups RNA polymerase V complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex nuclear DNA-directed RNA polymerase complex
L [auth E]	RNA polymerase subunit H/Rpb5 C-terminal domain-containing protein	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	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 transcription elongation by RNA polymerase I DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation biosynthetic process transcription by RNA polymerase I 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 transcription elongation by RNA polymerase I DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation biosynthetic process transcription by RNA polymerase I metabolic process cellular process macromolecule metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription by RNA polymerase III transcription by RNA polymerase II	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure RNA polymerase V complex organelle RNA polymerase complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure RNA polymerase V complex organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex membrane-enclosed lumen intracellular organelle lumen nuclear DNA-directed RNA polymerase complex nucleoplasm organelle lumen nuclear lumen
M [auth B]	DNA-directed RNA polymerase IV and V subunit 2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth C]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
E [auth C]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
E [auth C]	IPR050518	Archaeal Rpo3/Eukaryotic RPB3 RNA Polymerase Subunit	Family
E [auth C]	IPR022842	DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1	Family
E [auth C]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
E [auth C]	IPR001514	DNA-directed RNA polymerase, 30-40kDa subunit, conserved site	Conserved Site
E [auth C]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
F	IPR020708	DNA-directed RNA polymerase, 14-18kDa subunit, conserved site	Conserved Site
F	IPR028363	DNA-directed RNA polymerase, subunit RPB6	Family
F	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
F	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
F	IPR006111	Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit	Family
G [auth J]	IPR023580	RNA polymerase subunit RPB10	Homologous Superfamily
G [auth J]	IPR020789	RNA polymerases, subunit N, zinc binding site	Binding Site
G [auth J]	IPR000268	DNA-directed RNA polymerase subunit RPABC5/Rpb10	Family
H [auth K]	IPR022905	DNA-directed RNA polymerase subunit Rpo11-like	Family
H [auth K]	IPR009025	DNA-directed RNA polymerase, RBP11-like dimerisation domain	Domain
H [auth K]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
H [auth K]	IPR008193	DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site	Conserved Site
H [auth K]	IPR037685	RNA polymerase RBP11	Family
I [auth L]	IPR006591	RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4	Family
I [auth L]	IPR029040	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Homologous Superfamily
I [auth L]	IPR039747	DNA-directed RNA polymerases I, II, and III subunit RPABC4	Family
J [auth H]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
J [auth H]	IPR005570	DNA-directed RNA polymerases I, II, and III subunit RPABC3	Family
K [auth I]	IPR001529	DNA-directed RNA polymerase II subunit RPB9-like, zinc ribbon	Domain
K [auth I]	IPR012164	DNA-directed RNA polymerase subunit/transcription factor S	Family
K [auth I]	IPR001222	Zinc finger, TFIIS-type	Domain
K [auth I]	IPR034012	Pol II subunit B9, C-terminal zinc ribbon	Domain
K [auth I]	IPR019761	DNA-directed RNA polymerase M, 15kDa subunit, conserved site	Conserved Site
L [auth E]	IPR014381	DNA-directed RNA polymerase subunit Rpo5/Rpb5	Family
L [auth E]	IPR035913	RPB5-like RNA polymerase subunit superfamily	Homologous Superfamily
L [auth E]	IPR036710	RNA polymerase Rpb5, N-terminal domain superfamily	Homologous Superfamily
L [auth E]	IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	Domain
L [auth E]	IPR005571	RNA polymerase, Rpb5, N-terminal	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9K17 | pdb_00009k17

A cryo-EM structure of B. oleracea RNA polymerase V in complex with 6U sacffold at 3.04 Angstrom

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

9K17 | pdb_00009k17