+Open data
-Basic information
Entry | Database: PDB / ID: 8vq4 | |||||||||
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Title | CDK2-CyclinE1 in complex with allosteric inhibitor I-125A. | |||||||||
Components |
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Keywords | CELL CYCLE/TRANSFERASE/INHIBITOR / kinase / CELL CYCLE-TRANSFERASE-INHIBITOR complex | |||||||||
Function / homology | Function and homology information positive regulation of mesenchymal stem cell proliferation / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / G1/S-Specific Transcription / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation ...positive regulation of mesenchymal stem cell proliferation / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / G1/S-Specific Transcription / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / Association of TriC/CCT with target proteins during biosynthesis / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / DNA replication initiation / Activation of the pre-replicative complex / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / cyclin-dependent kinase / Cajal body / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / telomere maintenance / cyclin binding / post-translational protein modification / meiotic cell cycle / positive regulation of DNA replication / response to organic substance / male germ cell nucleus / G1/S transition of mitotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Wnt signaling pathway / Meiotic recombination / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / regulation of protein localization / G2/M transition of mitotic cell cycle / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / kinase activity / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / DNA replication / chromosome, telomeric region / regulation of cell cycle / endosome / chromatin remodeling / cell division / protein domain specific binding / protein phosphorylation / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Hirschi, M. / Johnson, E. / Zhang, Y. / Liu, Z. / Brodsky, O. / Won, S.J. / Nagata, A. / Petroski, M.D. / Majmudar, J.D. / Niessen, S. ...Hirschi, M. / Johnson, E. / Zhang, Y. / Liu, Z. / Brodsky, O. / Won, S.J. / Nagata, A. / Petroski, M.D. / Majmudar, J.D. / Niessen, S. / VanArsdale, T. / Gilbert, A.M. / Hayward, M.M. / Stewart, A.E. / Nager, A.R. / Melillo, B. / Cravatt, B. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biorxiv / Year: 2024 Title: Expanding the ligandable proteome by paralog hopping with covalent probes. Authors: Zhang, Y. / Liu, Z. / Hirschi, M. / Brodsky, O. / Johnson, E. / Won, S.J. / Nagata, A. / Petroski, M.D. / Majmudar, J.D. / Niessen, S. / VanArsdale, T. / Gilbert, A.M. / Hayward, M.M. / ...Authors: Zhang, Y. / Liu, Z. / Hirschi, M. / Brodsky, O. / Johnson, E. / Won, S.J. / Nagata, A. / Petroski, M.D. / Majmudar, J.D. / Niessen, S. / VanArsdale, T. / Gilbert, A.M. / Hayward, M.M. / Stewart, A.E. / Nager, A.R. / Melillo, B. / Cravatt, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vq4.cif.gz | 264.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vq4.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8vq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/8vq4 ftp://data.pdbj.org/pub/pdb/validation_reports/vq/8vq4 | HTTPS FTP |
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-Related structure data
Related structure data | 8vq3C 7kjsS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34056.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24941, cyclin-dependent kinase |
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#2: Protein | Mass: 33053.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNE1, CCNE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24864 |
#3: Chemical | ChemComp-A1AC5 / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.94 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.21 M sodium citrate tribasic dihydrate, 19.5% PEG3350 |
-Data collection
Diffraction | Mean temperature: 98.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 8, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.842→84.271 Å / Num. obs: 63226 / % possible obs: 79.5 % / Redundancy: 12.4 % / Biso Wilson estimate: 43.15 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rsym value: 0.059 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.896→2.055 Å / Redundancy: 11.4 % / Rmerge(I) obs: 4.64 / Num. unique obs: 329 / CC1/2: 0.653 / % possible all: 18.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7KJS Resolution: 1.9→45.23 Å / SU ML: 0.218 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.6956 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→45.23 Å
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Refine LS restraints |
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LS refinement shell |
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