+Open data
-Basic information
Entry | Database: PDB / ID: 7xqk | ||||||
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Title | The Crystal Structure of CDK3 and CyclinE1 Complex from Biortus. | ||||||
Components |
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Keywords | CELL CYCLE / complex | ||||||
Function / homology | Function and homology information positive regulation of mesenchymal stem cell proliferation / G0 to G1 transition / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / G1/S-Specific Transcription / cyclin E1-CDK2 complex / negative regulation of Notch signaling pathway / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / p53-Dependent G1 DNA Damage Response ...positive regulation of mesenchymal stem cell proliferation / G0 to G1 transition / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / G1/S-Specific Transcription / cyclin E1-CDK2 complex / negative regulation of Notch signaling pathway / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / p53-Dependent G1 DNA Damage Response / PTK6 Regulates Cell Cycle / Association of TriC/CCT with target proteins during biosynthesis / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / glutathione transferase / G0 and Early G1 / glutathione transferase activity / DNA replication initiation / cyclin-dependent protein kinase holoenzyme complex / positive regulation of G1/S transition of mitotic cell cycle / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cyclin E associated events during G1/S transition / regulation of G2/M transition of mitotic cell cycle / telomere maintenance / cyclin binding / : / G1/S transition of mitotic cell cycle / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Wnt signaling pathway / Cyclin D associated events in G1 / regulation of protein localization / kinase activity / regulation of gene expression / cell population proliferation / cell division / protein phosphorylation / protein serine kinase activity / centrosome / DNA damage response / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Schistosoma japonicum (invertebrata) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Gui, W. / Wang, F. / Cheng, W. / Gao, J. / Huang, Y. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: The Crystal Structure of CDK3 and CyclinE1 Complex from Biortus. Authors: Gui, W. / Wang, F. / Cheng, W. / Gao, J. / Huang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xqk.cif.gz | 155.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xqk.ent.gz | 111.4 KB | Display | PDB format |
PDBx/mmJSON format | 7xqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/7xqk ftp://data.pdbj.org/pub/pdb/validation_reports/xq/7xqk | HTTPS FTP |
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-Related structure data
Related structure data | 4eojS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 61776.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma japonicum (invertebrata), (gene. exp.) Homo sapiens (human) Gene: CDK3, CDKN3 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P08515, UniProt: Q00526, glutathione transferase, cyclin-dependent kinase |
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#2: Protein | Mass: 35718.312 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 |
-Non-polymers , 4 types, 443 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-MES / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6M MgSO4, 0.1M MES pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18078 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.18078 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→44.5 Å / Num. obs: 49467 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.139 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.25→2.32 Å / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4563 / CC1/2: 0.797 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EOJ Resolution: 2.25→44.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.962 / SU ML: 0.099 / Cross valid method: FREE R-VALUE / ESU R: 0.162 / ESU R Free: 0.153 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.105 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→44.5 Å
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Refine LS restraints |
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LS refinement shell |
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