8BUB

Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	WD40 repeat-like	8051194	3001694	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	WD40 repeat-like	8051194	3001694	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	WD40 repeat-like	8051194	3001694	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)
H [auth E]	SCOP2B Superfamily	Protein kinase-like (PK-like)	8062460	3000066	SCOP2B (2022-06-29)
I [auth H]	SCOP2B Superfamily	Protein kinase-like (PK-like)	8062460	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8062460	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cyclin-like	8034370	3000768	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cyclin-like	8034372	3000768	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	Cyclin-like	8034370	3000768	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	Cyclin-like	8034372	3000768	SCOP2B (2022-06-29)
G [auth I]	SCOP2B Superfamily	Cyclin-like	8034372	3000768	SCOP2B (2022-06-29)
G [auth I]	SCOP2B Superfamily	Cyclin-like	8034370	3000768	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, F [auth G]	PF10433	Mono-functional DNA-alkylating methyl methanesulfonate N-term (MMS1_N)	Mono-functional DNA-alkylating methyl methanesulfonate N-term	-	Repeat
A, D, F [auth G]	PF03178	CPSF A subunit region (CPSF_A)	CPSF A subunit region	-	Repeat
B, H [auth E], I [auth H]	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain	-	Domain
C, E [auth F], G [auth I]	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, E [auth F], G [auth I]	PF21797	Cyclin-T2-like, C-terminal domain (CycT2-like_C)	Cyclin-T2-like, C-terminal domain	This domain is found at the C-terminal end of human Cyclin-T2 (CycT2) and similar animal sequences. CycT2 is the regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P ...	This domain is found at the C-terminal end of human Cyclin-T2 (CycT2) and similar animal sequences. CycT2 is the regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P-TEFB). This domain adopts s cyclin box fold consisting of five helices and a short C-terminal helix [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, F [auth G]	DNA damage-binding protein 1	ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding protein binding cullin family protein binding damaged DNA binding WD40-repeat domain binding protein domain specific binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process proteolysis involved in protein catabolic process proteolysis proteasomal protein catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process proteolysis involved in protein catabolic process proteolysis proteasomal protein catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process apoptotic process cell death programmed cell death protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of biological process negative regulation of reproductive process regulation of reproductive process reproductive process biological regulation negative regulation of biological process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of cellular process epigenetic programming in the zygotic pronuclei cellular biosynthetic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis regulation of biosynthetic process epigenetic programming of gene expression epigenetic regulation of gene expression cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process regulation of cell cycle phase transition regulation of cell cycle process cell cycle phase transition mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle mitotic cell cycle process cell cycle regulation of cell cycle mitotic cell cycle phase transition cell cycle process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA repair positive regulation of viral genome replication positive regulation of viral process positive regulation of biological process viral life cycle regulation of viral process regulation of viral life cycle viral genome replication viral process regulation of viral genome replication developmental process cellular developmental process cell development developmental process involved in reproduction programmed cell death involved in cell development cell differentiation anatomical structure development ectopic germ cell programmed cell death nucleotide-excision repair response to light stimulus cellular response to environmental stimulus cellular response to light stimulus cellular response to radiation response to UV UV-damage excision repair response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV monosaccharide metabolic process positive regulation of cellular metabolic process gluconeogenesis regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process positive regulation of gluconeogenesis carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process hexose biosynthetic process positive regulation of glucose metabolic process regulation of gluconeogenesis positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process positive regulation of cellular biosynthetic process glucose metabolic process rhythmic process circadian rhythm regulation of circadian rhythm negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular process positive regulation of protein metabolic process regulation of protein metabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process positive regulation of macromolecule metabolic process regulation of protein catabolic process biological process involved in interspecies interaction between organisms biological process involved in interaction with symbiont biological process involved in symbiotic interaction regulation by virus of viral protein levels in host cell positive regulation by virus of viral protein levels in host cell regulation of biological quality proteasome-mediated ubiquitin-dependent protein catabolic process regulation of developmental process negative regulation of developmental process exit from host cell viral release from host cell biological process involved in interaction with host meiotic chromosome segregation sexual reproduction non-membrane-bounded organelle assembly microtubule cytoskeleton organization female gamete generation meiotic cell cycle process gamete generation cellular component biogenesis cellular component assembly female meiotic nuclear division meiotic nuclear division chromosome segregation spindle organization organelle assembly organelle fission meiotic cell cycle multicellular organismal reproductive process meiotic spindle organization meiotic spindle assembly spindle assembly nuclear division organelle organization nuclear chromosome segregation microtubule-based process cytoskeleton organization spindle assembly involved in female meiosis cell surface receptor signaling pathway signaling cell communication signal transduction Wnt signaling pathway	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm intracellular organelle intracellular non-membrane-bounded organelle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm intracellular organelle intracellular non-membrane-bounded organelle chromosome chromosome, telomeric region chromosomal region non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex Cul4-RING E3 ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul4A-RING E3 ubiquitin ligase complex nucleoplasm site of double-strand break site of DNA damage Cul4B-RING E3 ubiquitin ligase complex
B, H [auth E], I [auth H]	Cyclin-dependent kinase 12	protein binding binding cyclin binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding protein binding binding cyclin binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups 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 cyclin-dependent protein kinase activity kinase binding enzyme binding protein kinase binding RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat kinase activity	negative regulation of stem cell differentiation developmental process regulation of biological process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of developmental process biological regulation negative regulation of biological process regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation negative regulation of cellular process negative regulation of stem cell differentiation developmental process regulation of biological process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of developmental process biological regulation negative regulation of biological process regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation negative regulation of cellular process cellular process negative regulation of cell differentiation 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 mRNA processing mRNA metabolic process RNA processing protein phosphorylation protein autophosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process RNA splicing regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation regulation of transferase activity regulation of MAP kinase activity regulation of primary metabolic process regulation of phosphate metabolic process regulation of protein metabolic process regulation of cellular metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process regulation of molecular function regulation of kinase activity regulation of protein serine/threonine kinase activity regulation of phosphorylation regulation of phosphorus metabolic process regulation of metabolic process positive regulation of macromolecule biosynthetic process 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 transcription by RNA polymerase II regulation of DNA-templated transcription elongation positive regulation of nucleobase-containing compound metabolic process regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular biosynthetic process DNA-templated transcription elongation positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex cyclin K-CDK12 complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex cyclin K-CDK12 complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen transcription elongation factor complex nuclear protein-containing complex cyclin/CDK positive transcription elongation factor complex carboxy-terminal domain protein kinase complex nuclear cyclin-dependent protein kinase holoenzyme complex
C, E [auth F], G [auth I]	Cyclin-K	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 protein binding binding kinase binding enzyme 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 protein binding binding kinase binding enzyme binding protein kinase binding RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat kinase activity cyclin-dependent protein serine/threonine kinase activator activity enzyme regulator activity protein serine/threonine kinase activator activity molecular function activator activity protein kinase regulator activity kinase activator activity enzyme activator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase activator activity kinase regulator activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process negative regulation by host of viral genome replication biological process involved in interspecies interaction between organisms modulation by host of symbiont process viral life cycle negative regulation by host of viral process modulation by host of viral genome replication biological process involved in symbiotic interaction modulation by host of viral process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process negative regulation by host of viral genome replication biological process involved in interspecies interaction between organisms modulation by host of symbiont process viral life cycle negative regulation by host of viral process modulation by host of viral genome replication biological process involved in symbiotic interaction modulation by host of viral process viral genome replication viral process biological process involved in interaction with symbiont regulation of cellular process positive regulation of DNA-templated transcription cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular 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 positive regulation of nucleobase-containing compound metabolic process cellular 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 regulation of cellular biosynthetic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of cellular biosynthetic process cell division regulation of signaling signaling regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication signal transduction 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 transcription elongation by RNA polymerase II positive regulation of transcription elongation by RNA polymerase II regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation regulation of cyclin-dependent protein kinase activity regulation of transferase activity regulation of cyclin-dependent protein serine/threonine kinase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process protein metabolic process cell cycle phosphorus metabolic process protein modification process regulation of cell cycle protein phosphorylation phosphorylation regulation of protein metabolic process regulation of protein kinase activity regulation of molecular function regulation of kinase activity macromolecule modification regulation of protein serine/threonine kinase activity regulation of phosphorylation regulation of phosphorus metabolic process	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex cyclin K-CDK12 complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex cyclin K-CDK12 complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular organelle lumen intracellular organelle nucleoplasm cyclin/CDK positive transcription elongation factor complex intracellular membrane-bounded organelle cellular anatomical entity organelle lumen carboxy-terminal domain protein kinase complex organelle nuclear cyclin-dependent protein kinase holoenzyme complex nuclear lumen cyclin K-CDK13 complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, F [auth G]	IPR018846	Cleavage/polyadenylation specificity factor, A subunit, N-terminal	Domain
A, D, F [auth G]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, D, F [auth G]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, D, F [auth G]	IPR004871	Cleavage/polyadenylation specificity factor, A subunit, C-terminal	Domain
A, D, F [auth G]	IPR050358	RSE1/DDB1/CFT1/CPSF1	Family
B, H [auth E], I [auth H]	IPR017441	Protein kinase, ATP binding site	Binding Site
B, H [auth E], I [auth H]	IPR000719	Protein kinase domain	Domain
B, H [auth E], I [auth H]	IPR050108	Cyclin-dependent kinase	Family
B, H [auth E], I [auth H]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B, H [auth E], I [auth H]	IPR008271	Serine/threonine-protein kinase, active site	Active Site
C, E [auth F], G [auth I]	IPR004367	Cyclin, C-terminal domain	Domain
C, E [auth F], G [auth I]	IPR006671	Cyclin, N-terminal	Domain
C, E [auth F], G [auth I]	IPR036915	Cyclin-like superfamily	Homologous Superfamily
C, E [auth F], G [auth I]	IPR043198	Cyclin/Cyclin-like subunit Ssn8	Family
C, E [auth F], G [auth I]	IPR013763	Cyclin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D, F [auth G]	Pharos: Q16531	Disease Exacerbation gastric cancer lung cancer xeroderma pigmentosum gastric neoplasm drug-induced liver injury hereditary diffuse gastric adenocarcinoma psoriasis
B, H [auth E], I [auth H]	Pharos: Q9NYV4	prostate cancer rheumatoid arthritis colorectal adenocarcinoma medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor psoriasis large cell medulloblastoma Neoplasm of uncertain or unknown behavior of ovary ovarian carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia osteosarcoma ovarian neoplasm Pick disease
C, E [auth F], G [auth I]	Pharos: O75909	malignant pancreatic neoplasm pancreatic ductal adenocarcinoma osteosarcoma psoriasis ovarian cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, H [auth E], I [auth H]	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

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.