8U9X

STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION AT 3.0 A OF T834P MUTANT USING A FREE-ELECTRON LASER

External Resource: Annotation

Domain Annotation: SCOP2 Classification
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	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8042682	3001330	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RPB6/omega subunit-like	8042688	3000189	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00623	RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)	RNA polymerase Rpb1, domain 2	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, domain 2, contains the active site ...	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, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].	Domain
A	PF04990	RNA polymerase Rpb1, domain 7 (RNA_pol_Rpb1_7)	RNA polymerase Rpb1, domain 7	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, domain 7, represents a mobile modu ...	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, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (Pfam:PF04561) [1,2].	Domain
A	PF05000	RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)	RNA polymerase Rpb1, domain 4	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, domain 4, represents the funnel do ...	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, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].	Domain
A	PF04983	RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)	RNA polymerase Rpb1, domain 3	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, domain 3, represents the pore doma ...	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, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].	Domain
A	PF04992	RNA polymerase Rpb1, domain 6 (RNA_pol_Rpb1_6)	RNA polymerase Rpb1, 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, domain 6, represents a mobile modu ...	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, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [1,2]. This family appears to be specific to the largest subunit of RNA polymerase II.	Domain
A	PF04998	RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)	RNA polymerase Rpb1, domain 5	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, domain 5, represents the discontin ...	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, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].	Domain
A	PF04997	RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)	RNA polymerase Rpb1, domain 1	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, domain 1, represents the clamp do ...	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, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2].	Domain
F	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	DNA-directed RNA polymerase II subunit RPB9	-	-	-
A	DNA-directed RNA polymerase II subunit RPB1	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 cation 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 cation binding ion binding metal ion binding small molecule binding	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 nucleic acid biosynthetic process transcription by RNA polymerase II 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 nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process cellular response to stimulus postreplication repair response to stimulus DNA synthesis involved in DNA repair cellular response to stress response to stress DNA repair translesion synthesis DNA metabolic process DNA damage response DNA biosynthetic process RNA-templated transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule ribonucleoprotein granule intracellular non-membrane-bounded organelle supramolecular complex non-membrane-bounded organelle cytoplasmic stress granule membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule ribonucleoprotein granule intracellular non-membrane-bounded organelle supramolecular complex non-membrane-bounded organelle cytoplasmic stress granule RNA polymerase II, holoenzyme protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen nucleoplasm RNA polymerase II, core complex catalytic complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
J	DNA-directed RNA polymerases II subunit RPABC5	-	-	-
K	DNA-directed RNA polymerase II subunit RPB11	-	-	-
L	DNA-directed RNA polymerases II subunit RPABC4	-	-	-
M [auth R]	MOL_ID: 13	-	-	-
N [auth T]	MOL_ID: 14	-	-	-
B	DNA-directed RNA polymerase subunit beta	-	-	-
C	DNA-directed RNA polymerase II subunit RPB3	-	-	-
D	DNA-directed RNA polymerase II subunit RPB4	-	-	-
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	-	-	-
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity RNA polymerase I 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	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis 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 cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis 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 nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription by RNA polymerase III nucleolar large rRNA transcription by RNA polymerase I transcription by RNA polymerase I rRNA transcription rRNA metabolic process DNA-templated transcription termination termination of RNA polymerase I transcription RNA-templated transcription termination of RNA polymerase III transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription initiation at RNA polymerase III promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I transcription initiation at RNA polymerase I promoter	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 non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity 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 non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle intracellular non-membrane-bounded organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex cytoplasm
G	DNA-directed RNA polymerase II subunit RPB7	-	-	-
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007081	RNA polymerase Rpb1, domain 5	Domain
A	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
A	IPR007075	RNA polymerase Rpb1, domain 6	Domain
A	IPR000684	RNA polymerase II, heptapeptide repeat, eukaryotic	Repeat
A	IPR007083	RNA polymerase Rpb1, domain 4	Domain
A	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
A	IPR006592	RNA polymerase, N-terminal	Domain
A	IPR007066	RNA polymerase Rpb1, domain 3	Domain
A	IPR007073	RNA polymerase Rpb1, domain 7	Domain
A	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
A	IPR038593	RNA polymerase Rpb1, domain 7 superfamily	Homologous Superfamily
A	IPR000722	RNA polymerase, alpha subunit	Domain
A	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
A	IPR007080	RNA polymerase Rpb1, domain 1	Domain
F	IPR028363	DNA-directed RNA polymerase, subunit RPB6	Family
F	IPR006111	Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit	Family
F	IPR020708	DNA-directed RNA polymerase, 14-18kDa subunit, conserved site	Conserved Site
F	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
F	IPR036161	RPB6/omega subunit-like 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.