7DKH

Crystal structure of the Ctr9/Paf1/Cdc73/Rtf1 quaternary complex

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	TPR_15	e7dkhA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TPR_15	ECOD (1.6)
E	TPR_15	e7dkhE1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TPR_15	ECOD (1.6)
I	TPR_15	e7dkhI1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TPR_15	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E, I	PF13181	Tetratricopeptide repeat (TPR_8)	Tetratricopeptide repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, F, J	RNA polymerase II-associated protein 1	chromatin binding binding basal transcription machinery binding RNA polymerase binding protein binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding phosphoprotein binding RNA polymerase II C-terminal domain binding RNA polymerase II C-terminal domain phosphoserine binding phosphoserine residue binding protein phosphorylated amino acid binding	negative regulation of cellular catabolic process catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy negative regulation of cellular metabolic process cellular catabolic process mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process negative regulation of cellular catabolic process catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy negative regulation of cellular metabolic process cellular catabolic process mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process negative regulation of autophagy of mitochondrion biological regulation regulation of cellular metabolic process regulation of mitophagy regulation of catabolic process negative regulation of mitophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy regulation of cellular catabolic process metabolic process cellular process regulation of metabolic process autophagy of mitochondrion sno(s)RNA transcription cellular biosynthetic 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 sno(s)RNA metabolic process macromolecule metabolic process snoRNA transcription by RNA polymerase II transcription by RNA polymerase II sno(s)RNA processing sno(s)RNA 3'-end processing RNA 3'-end processing RNA processing positive regulation of macromolecule biosynthetic process regulation of primary metabolic process transcription elongation by RNA polymerase I positive regulation of metabolic process regulation of RNA metabolic process transcription by RNA polymerase I rRNA transcription positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of DNA-templated transcription elongation positive regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process regulation of gene expression positive regulation of transcription elongation by RNA polymerase I regulation of macromolecule biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process rRNA metabolic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process nucleolar large rRNA transcription by RNA polymerase I regulation of macromolecule metabolic process regulation of cellular biosynthetic process DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase I positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process DNA-templated transcription termination ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis regulation of DNA recombination DNA recombination DNA metabolic process negative regulation of DNA recombination negative regulation of DNA metabolic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of DNA metabolic process cellular response to stimulus global genome nucleotide-excision repair response to stimulus cellular response to stress nucleotide-excision repair DNA damage response response to stress DNA repair mRNA 3'-end processing mRNA processing mRNA metabolic process mitotic cell cycle process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process transcription elongation by RNA polymerase II regulation of transcription by RNA polymerase II regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of transcription elongation by RNA polymerase II transcription-coupled nucleotide-excision repair regulation of cellular response to stress regulation of response to stress regulation of transcription-coupled nucleotide-excision repair regulation of DNA repair regulation of response to stimulus regulation of nucleotide-excision repair negative regulation of RNA biosynthetic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of cellular biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process transcription by RNA polymerase III nucleolar chromatin organization cellular component organization chromatin organization chromatin remodeling rDNA heterochromatin formation heterochromatin formation epigenetic regulation of gene expression negative regulation of gene expression nucleus organization organelle organization nucleolus organization facultative heterochromatin formation negative regulation of gene expression, epigenetic	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm catalytic complex intracellular membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm catalytic complex intracellular membrane-bounded organelle cellular anatomical entity Cdc73/Paf1 complex 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 euchromatin intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle
C, G, K	Cell division control protein 73	basal transcription machinery binding RNA polymerase binding protein binding binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding chromatin binding phosphoprotein binding RNA polymerase II C-terminal domain binding RNA polymerase II C-terminal domain phosphoserine binding phosphoserine residue binding protein phosphorylated amino acid binding	cellular biosynthetic process mRNA 3'-end processing cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process cellular biosynthetic process mRNA 3'-end processing cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process transcription elongation by RNA polymerase II DNA-templated transcription DNA-templated transcription elongation transcription by RNA polymerase II regulation of cellular process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process transcription elongation by RNA polymerase I positive regulation of metabolic process regulation of RNA metabolic process transcription by RNA polymerase I rRNA transcription positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of DNA-templated transcription elongation regulation of biological process positive regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase I regulation of cellular metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of transcription elongation by RNA polymerase I regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process rRNA metabolic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process nucleolar large rRNA transcription by RNA polymerase I biological regulation regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of transcription elongation by RNA polymerase I positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process regulation of transcription by RNA polymerase II regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of transcription elongation by RNA polymerase II cellular response to stimulus response to stimulus transcription-coupled nucleotide-excision repair regulation of cellular response to stress cellular response to stress nucleotide-excision repair response to stress regulation of response to stress DNA repair regulation of transcription-coupled nucleotide-excision repair DNA metabolic process regulation of DNA repair DNA damage response regulation of response to stimulus regulation of nucleotide-excision repair regulation of DNA metabolic process regulation of DNA recombination negative regulation of metabolic process DNA recombination negative regulation of biological process negative regulation of DNA recombination negative regulation of DNA metabolic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process	intracellular organelle intracellular anatomical structure organelle euchromatin intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex transcription elongation factor complex nucleus intracellular organelle intracellular anatomical structure organelle euchromatin intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen nucleoplasm catalytic complex intracellular membrane-bounded organelle Cdc73/Paf1 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
D, H, L	RNA polymerase-associated protein RTF1	DNA binding binding organic cyclic compound binding nucleic acid binding phosphoprotein binding basal transcription machinery binding RNA polymerase binding RNA polymerase II C-terminal domain binding enzyme binding RNA polymerase II C-terminal domain phosphoserine binding protein binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding DNA binding binding organic cyclic compound binding nucleic acid binding phosphoprotein binding basal transcription machinery binding RNA polymerase binding RNA polymerase II C-terminal domain binding enzyme binding RNA polymerase II C-terminal domain phosphoserine binding protein binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding phosphoserine residue binding protein phosphorylated amino acid binding RNA binding	cellular biosynthetic process mRNA 3'-end processing cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process cellular biosynthetic process mRNA 3'-end processing cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process sexual reproduction reproductive process meiotic cell cycle DNA metabolic process meiotic cell cycle process meiotic DNA double-strand break formation meiosis I cell cycle process cell cycle cell cycle process sno(s)RNA transcription DNA-templated transcription sno(s)RNA metabolic process snoRNA transcription by RNA polymerase II transcription by RNA polymerase II sno(s)RNA processing sno(s)RNA 3'-end processing transcription elongation by RNA polymerase II DNA-templated transcription elongation regulation of cellular process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process transcription elongation by RNA polymerase I positive regulation of metabolic process regulation of RNA metabolic process transcription by RNA polymerase I rRNA transcription positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of DNA-templated transcription elongation regulation of biological process positive regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase I regulation of cellular metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of transcription elongation by RNA polymerase I regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process rRNA metabolic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process nucleolar large rRNA transcription by RNA polymerase I biological regulation regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of transcription elongation by RNA polymerase I positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process DNA-templated transcription termination regulation of transcription by RNA polymerase II regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of transcription elongation by RNA polymerase II cellular response to stimulus response to stimulus transcription-coupled nucleotide-excision repair regulation of cellular response to stress cellular response to stress nucleotide-excision repair response to stress regulation of response to stress DNA repair regulation of transcription-coupled nucleotide-excision repair regulation of DNA repair DNA damage response regulation of response to stimulus regulation of nucleotide-excision repair regulation of DNA metabolic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process global genome nucleotide-excision repair	intracellular organelle intracellular anatomical structure organelle euchromatin intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex transcription elongation factor complex nucleus intracellular organelle intracellular anatomical structure organelle euchromatin intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen nucleoplasm catalytic complex intracellular membrane-bounded organelle Cdc73/Paf1 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
A, E, I	RNA polymerase-associated protein CTR9	transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding DNA binding organic cyclic compound binding triplex DNA binding nucleic acid binding basal transcription machinery binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding DNA binding organic cyclic compound binding triplex DNA binding nucleic acid binding basal transcription machinery binding RNA polymerase binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding phosphoprotein binding RNA polymerase II C-terminal domain binding RNA polymerase II C-terminal domain phosphoserine binding phosphoserine residue binding protein phosphorylated amino acid binding	negative regulation of cellular catabolic process catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy negative regulation of cellular metabolic process cellular catabolic process mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process negative regulation of cellular catabolic process catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy negative regulation of cellular metabolic process cellular catabolic process mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process negative regulation of autophagy of mitochondrion biological regulation regulation of cellular metabolic process regulation of mitophagy regulation of catabolic process negative regulation of mitophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy regulation of cellular catabolic process metabolic process cellular process regulation of metabolic process autophagy of mitochondrion sno(s)RNA transcription cellular biosynthetic 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 sno(s)RNA metabolic process macromolecule metabolic process snoRNA transcription by RNA polymerase II transcription by RNA polymerase II sno(s)RNA processing sno(s)RNA 3'-end processing RNA 3'-end processing RNA processing positive regulation of macromolecule biosynthetic process regulation of primary metabolic process transcription elongation by RNA polymerase I positive regulation of metabolic process regulation of RNA metabolic process transcription by RNA polymerase I rRNA transcription positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of DNA-templated transcription elongation positive regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process regulation of gene expression positive regulation of transcription elongation by RNA polymerase I regulation of macromolecule biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process rRNA metabolic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process nucleolar large rRNA transcription by RNA polymerase I regulation of macromolecule metabolic process regulation of cellular biosynthetic process DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase I positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process DNA-templated transcription termination regulation of DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter regulation of transcription by RNA polymerase II DNA-templated transcription initiation regulation of transcription initiation by RNA polymerase II mRNA 3'-end processing mRNA processing mRNA metabolic process mitotic cell cycle process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process transcription elongation by RNA polymerase II cellular response to stimulus response to stimulus transcription-coupled nucleotide-excision repair regulation of cellular response to stress cellular response to stress nucleotide-excision repair response to stress regulation of response to stress DNA repair regulation of transcription-coupled nucleotide-excision repair DNA metabolic process regulation of DNA repair DNA damage response regulation of response to stimulus regulation of nucleotide-excision repair regulation of DNA metabolic process	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm catalytic complex intracellular membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm catalytic complex intracellular membrane-bounded organelle cellular anatomical entity Cdc73/Paf1 complex 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 euchromatin intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, F, J	IPR007133	RNA polymerase II associated factor Paf1	Family
C, G, K	IPR031336	Cell division control protein 73, C-terminal	Domain
C, G, K	IPR007852	Cdc73/Parafibromin	Family
C, G, K	IPR038103	Cell division control protein 73, C-terminal domain superfamily	Homologous Superfamily
D, H, L	IPR036128	Plus3-like superfamily	Homologous Superfamily
D, H, L	IPR004343	Plus-3 domain	Domain
A, E, I	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A, E, I	IPR031101	RNA polymerase-associated protein Ctr9	Family
A, E, I	IPR019734	Tetratricopeptide repeat	Repeat

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.