+Open data
-Basic information
Entry | Database: PDB / ID: 4y72 | ||||||
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Title | Human CDK1/CyclinB1/CKS2 With Inhibitor | ||||||
Components |
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Keywords | TRANSFERASE / CDK1 / CyclinB1 / CKS2 / Inhibitor | ||||||
Function / homology | Function and homology information regulation of Schwann cell differentiation / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / G2/M DNA replication checkpoint ...regulation of Schwann cell differentiation / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / positive regulation of attachment of spindle microtubules to kinetochore / MASTL Facilitates Mitotic Progression / regulation of mitotic cell cycle spindle assembly checkpoint / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / Phosphorylation of Emi1 / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / patched binding / Nuclear Pore Complex (NPC) Disassembly / Transcriptional regulation by RUNX2 / Phosphorylation of the APC/C / outer kinetochore / meiosis I / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Initiation of Nuclear Envelope (NE) Reformation / protein localization to kinetochore / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / cyclin-dependent protein serine/threonine kinase activator activity / Condensation of Prometaphase Chromosomes / response to copper ion / chromosome condensation / centrosome cycle / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / SCF ubiquitin ligase complex / mitotic metaphase chromosome alignment / G1/S-Specific Transcription / cyclin-dependent protein kinase activity / MAPK3 (ERK1) activation / response to amine / ubiquitin-like protein ligase binding / mitotic G2 DNA damage checkpoint signaling / Regulation of APC/C activators between G1/S and early anaphase / regulation of embryonic development / cellular response to organic cyclic compound / response to axon injury / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / Nuclear events stimulated by ALK signaling in cancer / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / response to cadmium ion / Cyclin A/B1/B2 associated events during G2/M transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle cell proliferation / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / epithelial cell differentiation / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / Hsp70 protein binding / APC/C:Cdc20 mediated degradation of Cyclin B / ERK1 and ERK2 cascade / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / Condensation of Prophase Chromosomes / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / mitotic spindle organization / positive regulation of DNA replication / ubiquitin binding / response to activity / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / peptidyl-threonine phosphorylation / MAPK6/MAPK4 signaling / PKR-mediated signaling / spindle microtubule / regulation of circadian rhythm / response to toxic substance / mitotic spindle / spindle pole / positive regulation of protein import into nucleus / microtubule cytoskeleton organization / cellular response to hydrogen peroxide / positive regulation of protein localization to nucleus / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Brown, N.R. / Korolchuk, S. / Martin, M.P. / Stanley, W. / Moukhametzianov, R. / Noble, M.E.M. / Endicott, J.A. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: CDK1 structures reveal conserved and unique features of the essential cell cycle CDK. Authors: Brown, N.R. / Korolchuk, S. / Martin, M.P. / Stanley, W.A. / Moukhametzianov, R. / Noble, M.E. / Endicott, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y72.cif.gz | 280.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y72.ent.gz | 226.9 KB | Display | PDB format |
PDBx/mmJSON format | 4y72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4y72_validation.pdf.gz | 738.7 KB | Display | wwPDB validaton report |
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Full document | 4y72_full_validation.pdf.gz | 742.7 KB | Display | |
Data in XML | 4y72_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 4y72_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/4y72 ftp://data.pdbj.org/pub/pdb/validation_reports/y7/4y72 | HTTPS FTP |
-Related structure data
Related structure data | 4yc3C 4yc6C 5hq0C 1hckS 1jstS 2b9rS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34553.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK1, CDC2, CDC28A, CDKN1, P34CDC2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P06493, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase |
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#2: Protein | Mass: 31369.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNB1, CCNB / Plasmid: PET-28 A+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CODONPLUS RIL / References: UniProt: P14635 |
#3: Protein | Mass: 10290.819 Da / Num. of mol.: 1 / Fragment: residues 165-433 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CKS2 / Plasmid: GST-3C / Production host: Escherichia coli (E. coli) / References: UniProt: P33552 |
#4: Chemical | ChemComp-LZ9 / {[( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.7 Details: Conditions around 0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97957 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97957 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→53 Å / Num. all: 34085 / Num. obs: 34085 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1hck, 2b9r, 1jst Resolution: 2.3→53 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.85 Å2 / Biso mean: 48.7092 Å2 / Biso min: 20.26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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