+Open data
-Basic information
Entry | Database: PDB / ID: 6gu2 | |||||||||
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Title | CDK1/CyclinB/Cks2 in complex with Flavopiridol | |||||||||
Components |
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Keywords | CELL CYCLE / 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 / Phosphorylation of Emi1 / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / patched binding / cyclin A2-CDK1 complex / Transcriptional regulation by RUNX2 / Nuclear Pore Complex (NPC) Disassembly / 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 / chromosome condensation / response to copper ion / 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 / cyclin-dependent protein kinase holoenzyme complex / response to axon injury / cyclin-dependent kinase / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / response to cadmium ion / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin A/B1/B2 associated events during G2/M transition / positive regulation of cardiac muscle cell proliferation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / ERK1 and ERK2 cascade / Hsp70 protein binding / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / epithelial cell differentiation / APC/C:Cdc20 mediated degradation of Cyclin B / regulation of mitotic cell cycle / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / cyclin binding / positive regulation of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / AURKA Activation by TPX2 / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Condensation of Prophase Chromosomes / response to activity / positive regulation of DNA replication / ubiquitin binding / spindle microtubule / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / G1/S transition of mitotic cell cycle / peptidyl-threonine phosphorylation / MAPK6/MAPK4 signaling / PKR-mediated signaling / regulation of circadian rhythm / mitotic spindle / microtubule cytoskeleton organization / response to toxic substance / cellular response to hydrogen peroxide / spindle pole / positive regulation of protein import into nucleus / positive regulation of protein localization to nucleus / The role of GTSE1 in G2/M progression after G2 checkpoint / rhythmic process / G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / 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 Å | |||||||||
Authors | Wood, D.J. / Korolchuk, S. / Tatum, N.J. / Wang, L.Z. / Endicott, J.A. / Noble, M.E.M. / Martin, M.P. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Cell Chem Biol / Year: 2019 Title: Differences in the Conformational Energy Landscape of CDK1 and CDK2 Suggest a Mechanism for Achieving Selective CDK Inhibition. Authors: Wood, D.J. / Korolchuk, S. / Tatum, N.J. / Wang, L.Z. / Endicott, J.A. / Noble, M.E.M. / Martin, M.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gu2.cif.gz | 147.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gu2.ent.gz | 113.1 KB | Display | PDB format |
PDBx/mmJSON format | 6gu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/6gu2 ftp://data.pdbj.org/pub/pdb/validation_reports/gu/6gu2 | HTTPS FTP |
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-Related structure data
Related structure data | 6gu3C 6gu4C 6gu6C 6gu7C 6gubC 6gucC 6gueC 6gufC 6guhC 6gukC 4y72S 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 / Plasmid: pVL1393 / 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: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14635 |
#3: Protein | Mass: 10290.819 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CKS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P33552, UniProt: K9J4F7*PLUS |
#4: Chemical | ChemComp-F9Z / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.96 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2→89.17 Å / Num. obs: 50412 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y72 Resolution: 2→89.17 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.163 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.989 Å2
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Refinement step | Cycle: 1 / Resolution: 2→89.17 Å
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Refine LS restraints |
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