7JV7 | pdb_00007jv7

Crystal Structure of the yeast RNA Pol II CTD kinase CTDK-1 complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d7jv7a_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Protein kinases catalytic domain-like	8102434	4003661	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Protein kinase-like (PK-like)	8102435	3000066	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	CENP-T_C	e7jv7B1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CENP-T_C	ECOD (v294.1)
A	CENP-T_C	e7jv7A1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CENP-T_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.472.10	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF12350	CTD kinase subunit gamma CTK3 C-terminus (CTK3_C)	CTD kinase subunit gamma CTK3 C-terminus	The C-terminal domain kinase (CTDK-1), is a three-subunit complex comprised of Ctk1, Ctk2, and Ctk3, that plays a key role in regulation of transcription and translation and in coordinating these two processes. Both Ctk2 and Ctk3 are regulated at the ...	The C-terminal domain kinase (CTDK-1), is a three-subunit complex comprised of Ctk1, Ctk2, and Ctk3, that plays a key role in regulation of transcription and translation and in coordinating these two processes. Both Ctk2 and Ctk3 are regulated at the level of protein turnover, and are unstable proteins processed through a ubiquitin-proteasome pathway. Their physical interaction is required to protect both subunits from degradation, and both Ctk2 and Ctk3 are required for Ctk1 CTD kinase activation [1]. The mammalian P-TEFb is mirrored by the combined complexes in yeast of the CTDK1 and the Bur1/2 [2]. It is not clear what independent function this C-terminal domain has.	Domain
B	PF00134	Cyclin, N-terminal domain (Cyclin_N)	Cyclin, N-terminal domain	Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins [4]. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.	Domain
A	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	CTD kinase subunit gamma	enzyme regulator activity cyclin-dependent protein serine/threonine kinase regulator activity cyclin-dependent protein kinase regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process mRNA 3'-end processing 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 RNA processing macromolecule metabolic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of DNA-templated transcription elongation regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of protein metabolic process positive regulation of translation protein biosynthetic process post-transcriptional regulation of gene expression positive regulation of translational fidelity protein metabolic process regulation of biological quality regulation of protein metabolic process translation positive regulation of gene expression regulation of translation regulation of translational fidelity transcription by RNA polymerase I positive regulation of transcription by RNA polymerase I regulation of transcription by RNA polymerase I transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of 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 protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure carboxy-terminal domain protein kinase complex organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure carboxy-terminal domain protein kinase complex organelle serine/threonine protein kinase complex membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen transcription elongation factor complex nucleoplasm cyclin/CDK positive transcription elongation factor complex cyclin-dependent protein kinase holoenzyme complex CTDK-1 complex nuclear cyclin-dependent protein kinase holoenzyme complex cytoplasm
B	CTD kinase subunit beta	enzyme regulator activity cyclin-dependent protein serine/threonine kinase regulator activity cyclin-dependent protein kinase regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity cyclin-dependent protein serine/threonine kinase activator activity protein serine/threonine kinase activator activity molecular function activator activity kinase activator activity enzyme activator activity protein kinase activator activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process mRNA 3'-end processing 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 RNA processing macromolecule metabolic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of DNA-templated transcription elongation regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of protein metabolic process positive regulation of translation protein biosynthetic process post-transcriptional regulation of gene expression positive regulation of translational fidelity protein metabolic process regulation of biological quality regulation of protein metabolic process translation positive regulation of gene expression regulation of translation regulation of translational fidelity transcription by RNA polymerase I positive regulation of transcription by RNA polymerase I regulation of transcription by RNA polymerase I transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of 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 protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure carboxy-terminal domain protein kinase complex organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure carboxy-terminal domain protein kinase complex organelle serine/threonine protein kinase complex membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen transcription elongation factor complex nucleoplasm cyclin/CDK positive transcription elongation factor complex cyclin-dependent protein kinase holoenzyme complex nuclear cyclin-dependent protein kinase holoenzyme complex cytoplasm cytosol CTDK-1 complex
A	CTD kinase subunit alpha	protein binding binding cyclin 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 protein binding binding cyclin 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 protein serine/threonine kinase activity cyclin-dependent protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity cyclin-dependent protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat kinase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process translational initiation metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process translational initiation metabolic process protein metabolic process macromolecule metabolic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of DNA-templated transcription elongation regulation of biological process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process mRNA 3'-end processing mRNA processing mRNA metabolic process RNA 3'-end processing RNA processing positive regulation of protein metabolic process positive regulation of translation post-transcriptional regulation of gene expression positive regulation of translational fidelity regulation of biological quality regulation of protein metabolic process positive regulation of gene expression regulation of translation regulation of translational fidelity transcription by RNA polymerase I positive regulation of transcription by RNA polymerase I regulation of transcription by RNA polymerase I transcription elongation by RNA polymerase II positive regulation of transcription elongation by RNA polymerase II transcription 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	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure carboxy-terminal domain protein kinase complex organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure carboxy-terminal domain protein kinase complex organelle serine/threonine protein kinase complex membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen transcription elongation factor complex nucleoplasm cyclin/CDK positive transcription elongation factor complex cyclin-dependent protein kinase holoenzyme complex nuclear cyclin-dependent protein kinase holoenzyme complex CTDK-1 complex cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR042326	CTD kinase subunit gamma	Family
C	IPR024637	CTD kinase subunit gamma Ctk3, C-terminal	Domain
B	IPR006671	Cyclin, N-terminal	Domain
B	IPR036915	Cyclin-like superfamily	Homologous Superfamily
B	IPR043198	Cyclin/Cyclin-like subunit Ssn8	Family
B	IPR013763	Cyclin-like domain	Domain
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR000719	Protein kinase domain	Domain
A	IPR050108	Cyclin-dependent kinase	Family
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site

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.