Annotations: 9R2I

Cryo-EM structure of the complex CDK16:CCNY:14-3-3

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)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8062585	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	14-3-3 protein	8082815	3001329	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	14-3-3 protein	8082815	3001329	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	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	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain
A, B	PF00244	14-3-3 protein (14-3-3)	14-3-3 protein	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	Cyclin-Y	protein binding binding kinase binding enzyme binding protein kinase binding 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 protein binding binding kinase binding enzyme binding protein kinase binding 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 regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus regulation of Wnt signaling pathway signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway biological regulation regulation of signal transduction cell communication regulation of response to stimulus cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus regulation of Wnt signaling pathway signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway biological regulation regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication cellular process signal transduction Wnt signaling pathway developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cell division regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process positive regulation of cyclin-dependent protein kinase activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of molecular function positive regulation of protein serine/threonine kinase activity positive regulation of protein modification process positive regulation of cyclin-dependent protein serine/threonine kinase activity regulation of cyclin-dependent protein serine/threonine kinase activity phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process cell cycle positive regulation of protein kinase activity protein modification process positive regulation of protein phosphorylation regulation of cell cycle positive regulation of cellular process protein phosphorylation phosphorylation regulation of protein metabolic process positive regulation of catalytic activity primary metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process positive regulation of cell cycle regulation of molecular function positive regulation of kinase activity regulation of kinase activity macromolecule modification regulation of protein serine/threonine kinase activity regulation of phosphorylation metabolic process macromolecule metabolic process regulation of metabolic process cell cycle G2/M phase transition mitotic cell cycle process G2/M transition of mitotic cell cycle cell cycle phase transition mitotic cell cycle cell cycle process mitotic cell cycle phase transition positive regulation of autophagy catabolic process autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process process utilizing autophagic mechanism	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex catalytic complex cyclin-dependent protein kinase holoenzyme complex cytoplasmic cyclin-dependent protein kinase holoenzyme complex transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups serine/threonine protein kinase complex cytoplasm cell periphery plasma membrane membrane nucleoplasm
C	Cyclin-dependent kinase 16	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 binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate 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 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 cyclin-dependent protein kinase activity	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of biological process regulation of cell cycle phase transition regulation of cellular process regulation of cell cycle process biological regulation cell cycle phase transition developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of biological process regulation of cell cycle phase transition regulation of cellular process regulation of cell cycle process biological regulation cell cycle phase transition cellular process cell cycle regulation of cell cycle cell cycle process cellular response to stimulus regulation of localization establishment of protein localization nitrogen compound transport response to stimulus cell communication localization carbohydrate homeostasis establishment of localization in cell intracellular protein localization regulation of biological quality regulation of peptide hormone secretion regulation of hormone levels establishment of protein localization to extracellular region intracellular glucose homeostasis protein secretion establishment of localization cellular response to oxygen-containing compound regulation of protein secretion regulation of secretion cellular response to carbohydrate stimulus chemical homeostasis response to glucose response to chemical glucose homeostasis insulin secretion involved in cellular response to glucose stimulus cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport signaling homeostatic process hormone secretion protein localization to extracellular region peptide secretion regulation of secretion by cell secretion by cell response to monosaccharide response to carbohydrate signal release cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus regulation of signaling regulation of transport secretion regulation of peptide transport regulation of establishment of protein localization export from cell cell-cell signaling response to oxygen-containing compound cellular response to glucose stimulus regulation of protein transport peptide transport response to hexose cellular response to chemical stimulus cellular homeostasis regulation of cellular localization protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization regulation of insulin secretion involved in cellular response to glucose stimulus hormone transport regulation of cell communication insulin secretion protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process exocytosis vesicle-mediated transport growth hormone secretion positive regulation of autophagy catabolic process autophagy positive regulation of biological process regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process process utilizing autophagic mechanism regulation of metabolic process positive regulation of cellular process multicellular organismal process plasma membrane bounded cell projection organization cellular developmental process cell projection organization cell development neuron projection development nervous system development cellular component organization generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation neuron development anatomical structure development cellular component organization or biogenesis system development	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane cell projection neuron projection plasma membrane bounded cell projection cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane membrane-bounded organelle transport vesicle synapse intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle presynapse cytoplasmic vesicle synaptic vesicle organelle cell junction secretory vesicle vesicle exocytic vesicle nucleus
A, B	14-3-3 protein eta	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding binding nuclear glucocorticoid receptor binding DNA-binding transcription factor binding protein domain specific binding protein heterodimerization activity protein dimerization activity transmembrane transporter binding channel regulator activity ion channel regulator activity molecular function regulator activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding binding nuclear glucocorticoid receptor binding DNA-binding transcription factor binding protein domain specific binding protein heterodimerization activity protein dimerization activity transmembrane transporter binding channel regulator activity ion channel regulator activity molecular function regulator activity sodium channel regulator activity transporter regulator activity cytoskeletal protein binding actin binding enzyme binding identical protein binding insulin-like growth factor receptor binding signaling receptor binding	trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process modulation of chemical synaptic transmission signaling biological regulation cell-cell signaling presynaptic modulation of chemical synaptic transmission chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process modulation of chemical synaptic transmission signaling biological regulation cell-cell signaling presynaptic modulation of chemical synaptic transmission chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication cellular process glucocorticoid metabolic process steroid catabolic process lipid catabolic process catabolic process glucocorticoid catabolic process steroid metabolic process metabolic process primary metabolic process lipid metabolic process cellular response to stimulus intracellular receptor signaling pathway response to stimulus response to lipid hormone-mediated signaling pathway intracellular signal transduction cellular response to endogenous stimulus response to hormone response to steroid hormone signal transduction nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus response to endogenous stimulus nuclear receptor-mediated corticosteroid signaling pathway cellular response to chemical stimulus response to chemical cellular response to lipid nuclear receptor-mediated signaling pathway nuclear receptor-mediated glucocorticoid signaling pathway membrane depolarization during action potential membrane depolarization action potential regulation of biological quality regulation of membrane potential multicellular organismal process cell projection organization negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation regulation of dendrite morphogenesis anatomical structure development system development developmental process negative regulation of cellular component organization regulation of cell projection organization nervous system development generation of neurons regulation of dendrite development negative regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization regulation of developmental process cellular developmental process plasma membrane bounded cell projection morphogenesis cell development cell morphogenesis regulation of nervous system development cellular component organization negative regulation of neurogenesis neurogenesis dendrite development negative regulation of cellular process negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation cellular component organization or biogenesis negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of multicellular organismal development plasma membrane bounded cell projection organization negative regulation of dendrite morphogenesis negative regulation of developmental process dendrite morphogenesis cell morphogenesis involved in neuron differentiation negative regulation of cell development anatomical structure morphogenesis neuron development regulation of plasma membrane bounded cell projection organization cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization intracellular protein localization intracellular protein transport head development animal organ development brain development substantia nigra development central nervous system development midbrain development neural nucleus development regulation of neuron differentiation regulation of synaptic plasticity 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 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 macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process regulation of localization regulation of transport regulation of monoatomic ion transport regulation of sodium ion transport metal ion transport monoatomic ion transport regulation of metal ion transport monoatomic cation transport sodium ion transport	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region vesicle extracellular membrane-bounded organelle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region vesicle extracellular membrane-bounded organelle cytosol cell periphery plasma membrane membrane presynapse synapse cell junction neuron to neuron synapse asymmetric synapse cerebellar granule cell to Purkinje cell synapse glutamatergic synapse excitatory synapse asymmetric, glutamatergic, excitatory synapse cell-cell junction intercalated disc anchoring junction cell-cell contact zone

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR006671	Cyclin, N-terminal	Domain
D	IPR012399	Cyclin Y	Family
D	IPR036915	Cyclin-like superfamily	Homologous Superfamily
D	IPR013763	Cyclin-like domain	Domain
C	IPR017441	Protein kinase, ATP binding site	Binding Site
C	IPR000719	Protein kinase domain	Domain
C	IPR050108	Cyclin-dependent kinase	Family
C	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C	IPR008271	Serine/threonine-protein kinase, active site	Active Site
A, B	IPR023409	14-3-3 protein, conserved site	Conserved Site
A, B	IPR023410	14-3-3 domain	Domain
A, B	IPR036815	14-3-3 domain superfamily	Homologous Superfamily
A, B	IPR000308	14-3-3 protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D	: Q8ND76	ulcerative colitis Crohn disease Regional enteritis amebiasis glioblastoma malignant ependymoma oligodendroglioma pancreatic ductal adenocarcinoma rheumatoid arthritis astrocytic tumor Crohn's colitis cystic fibrosis ileocolitis malignant glioma osteosarcoma ulcerative colitis Crohn disease Regional enteritis amebiasis glioblastoma malignant ependymoma oligodendroglioma pancreatic ductal adenocarcinoma rheumatoid arthritis astrocytic tumor Crohn's colitis cystic fibrosis ileocolitis malignant glioma osteosarcoma primitive neuroectodermal tumor tuberculosis atypical teratoid rhabdoid tumor eosinophilic esophagitis large cell medulloblastoma medulloblastoma ovarian cancer
C	: Q00536	acute myeloid leukemia intellectual disability large cell medulloblastoma Malignant Melanoma with BRAF V600E Mutation pilocytic astrocytoma schizophrenia breast cancer malignant ependymoma psoriasis idiopathic pulmonary fibrosis interstitial lung disease malignant glioma non-small cell lung carcinoma rheumatoid arthritis subependymal giant cell astrocytoma
A, B	: Q04917	cardiomyopathy Diabetes Mellitus, Experimental pilocytic astrocytoma bipolar disorder IgA glomerulonephritis malignant ependymoma pancreatic ductal adenocarcinoma primitive neuroectodermal tumor subependymal giant cell astrocytoma astrocytic tumor glioblastoma large cell medulloblastoma malignant glioma myopathy Pick disease cardiomyopathy Diabetes Mellitus, Experimental pilocytic astrocytoma bipolar disorder IgA glomerulonephritis malignant ependymoma pancreatic ductal adenocarcinoma primitive neuroectodermal tumor subependymal giant cell astrocytoma astrocytic tumor glioblastoma large cell medulloblastoma malignant glioma myopathy Pick disease schizophrenia atypical teratoid rhabdoid tumor hepatitis C virus infection lung adenocarcinoma medulloblastoma oligodendroglioma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D	SEP	Parent Component: SER : AA0037 : O-phospho-L-serine MOD:00046

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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.