Annotations: 7KPX

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Pkinase_Tyr	e7kpxA1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
B	Cyclin_N_1	e7kpxB1	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: Cyclin_N_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
C	PF09497	Transcription mediator complex subunit Med12 (Med12)	Transcription mediator complex subunit Med12	Med12 is a negative regulator of the Gli3-dependent sonic hedgehog signalling pathway via its interaction with Gli3 within the RNA polymerase II transcriptional Mediator. A complex is formed between Med12, Med13, CDK8 and CycC which is responsible fo ...	Med12 is a negative regulator of the Gli3-dependent sonic hedgehog signalling pathway via its interaction with Gli3 within the RNA polymerase II transcriptional Mediator. A complex is formed between Med12, Med13, CDK8 and CycC which is responsible for suppression of transcription. This subunit forms part of the Kinase section of Mediator [2].	Domain
D	PF11597	Mediator complex subunit 13 N-terminal (Med13_N)	Mediator complex subunit 13 N-terminal	Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [1-2]. It is arranged into four different sections, a core, a head, a t ...	Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood [4].	Domain
D	PF06333	Mediator complex subunit 13 C-terminal domain (Med13_C)	Mediator complex subunit 13 C-terminal domain	Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [1-2]. It is arranged into four different sections, a core, a head, a t ...	Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood [4]. This domain is also identified as an RNaseH domain of the medPIWI PIWI/Argonaute module. medPIWI is the core domain found in the Med13 protein. The medPIWI module in Med13 is predicted to bind double-stranded nucleic acids, triggering the experimentally-observed conformational switch in the CDK8 subcomplex which regulates the Mediator complex [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Meiotic mRNA stability protein kinase SSN3	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound 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 cation binding metal ion binding protein serine kinase activity	regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation nuclear-transcribed mRNA catabolic process, non-stop decay regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process negative regulation of cellular biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process protein destabilization regulation of protein stability regulation of biological quality cellular response to stimulus response to stimulus regulation of transcription from RNA polymerase II promoter by galactose carbon catabolite regulation of transcription positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by galactose positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process cellular response to nutrient levels carbon catabolite regulation of transcription from RNA polymerase II promoter carbon catabolite activation of transcription from RNA polymerase II promoter response to chemical regulation of DNA-templated transcription carbon catabolite activation of transcription response to nutrient levels positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of transcription by galactose response to nutrient nucleobase-containing compound biosynthetic process positive regulation of transcription from RNA polymerase II promoter by galactose cellular response to chemical stimulus positive regulation of RNA biosynthetic process cellular response to nutrient positive regulation of cellular biosynthetic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process sexual reproduction reproductive process meiotic cell cycle cell cycle regulation of growth negative regulation of growth negative regulation of filamentous growth regulation of filamentous growth growth filamentous growth	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus cyclin-dependent protein kinase holoenzyme complex nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus cyclin-dependent protein kinase holoenzyme complex nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle CKM complex serine/threonine protein kinase complex nuclear cyclin-dependent protein kinase holoenzyme complex mediator complex
B	RNA polymerase II holoenzyme cyclin-like subunit	enzyme regulator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding core promoter sequence-specific DNA binding nucleic acid binding RNA polymerase II core promoter sequence-specific DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding enzyme regulator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding core promoter sequence-specific DNA binding nucleic acid binding RNA polymerase II core promoter sequence-specific DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding	cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus cellular process response to temperature stimulus regulation of cellular process carbon catabolite regulation of transcription positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus cellular process response to temperature stimulus regulation of cellular process carbon catabolite regulation of transcription positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA-templated transcription positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by galactose cellular metabolic process primary metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process regulation of gene expression cellular response to nutrient levels biosynthetic process response to chemical metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process carbon catabolite activation of transcription response to nutrient levels cellular biosynthetic process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of cellular process regulation of transcription by galactose regulation of RNA biosynthetic process regulation of biosynthetic process biological regulation response to nutrient regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process cellular response to chemical stimulus positive regulation of RNA biosynthetic process cellular response to nutrient positive regulation of cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II 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 sexual reproduction reproductive process meiotic cell cycle cell cycle positive regulation of transcription by RNA polymerase II	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus cyclin-dependent protein kinase holoenzyme complex nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus cyclin-dependent protein kinase holoenzyme complex nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle CKM complex serine/threonine protein kinase complex nuclear cyclin-dependent protein kinase holoenzyme complex mediator complex
C	Mediator of RNA polymerase II transcription subunit 12	transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity	regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process cellular response to stimulus response to stimulus carbon catabolite regulation of transcription positive regulation of transcription by galactose cellular response to nutrient levels response to chemical carbon catabolite activation of transcription response to nutrient levels regulation of transcription by galactose response to nutrient cellular response to chemical stimulus cellular response to nutrient	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus cyclin-dependent protein kinase holoenzyme complex nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus cyclin-dependent protein kinase holoenzyme complex nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle CKM complex serine/threonine protein kinase complex nuclear cyclin-dependent protein kinase holoenzyme complex mediator complex
D	Mediator of RNA polymerase II transcription subunit 13	transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding cyclin binding	regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular response to stimulus response to stimulus regulation of transcription from RNA polymerase II promoter by galactose carbon catabolite regulation of transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by galactose positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process cellular response to nutrient levels carbon catabolite regulation of transcription from RNA polymerase II promoter carbon catabolite activation of transcription from RNA polymerase II promoter response to chemical carbon catabolite activation of transcription response to nutrient levels positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process regulation of transcription by galactose response to nutrient positive regulation of transcription from RNA polymerase II promoter by galactose cellular response to chemical stimulus positive regulation of RNA biosynthetic process cellular response to nutrient positive regulation of cellular biosynthetic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus cyclin-dependent protein kinase holoenzyme complex nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus cyclin-dependent protein kinase holoenzyme complex nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle CKM complex serine/threonine protein kinase complex nuclear cyclin-dependent protein kinase holoenzyme complex mediator complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR000719	Protein kinase domain	Domain
A	IPR050108	Cyclin-dependent kinase	Family
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site
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
C	IPR019035	Mediator complex, subunit Med12	Domain
D	IPR051139	Mediator complex subunit 13	Family
D	IPR021643	Mediator complex, subunit Med13, N-terminal	Domain
D	IPR009401	Mediator complex subunit Med13, C-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.