+Open data
-Basic information
Entry | Database: PDB / ID: 2jgz | ||||||
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Title | Crystal structure of phospho-CDK2 in complex with Cyclin B | ||||||
Components |
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Keywords | TRANSFERASE / PROTEIN KINASE / UBL CONJUGATION / PHOSPHORYLATION / SERINE/THREONINE-PROTEIN KINASE / KINASE / CYCLIN / MITOSIS / CELL CYCLE / ATP-BINDING / POLYMORPHISM / CELL DIVISION / NUCLEOTIDE-BINDING / SUBSTRATE SPECIFICITY | ||||||
Function / homology | Function and homology information cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / 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 ...cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / 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 / patched binding / Nuclear Pore Complex (NPC) Disassembly / Transcriptional regulation by RUNX2 / outer kinetochore / Phosphorylation of the APC/C / mitotic cell cycle phase transition / Initiation of Nuclear Envelope (NE) Reformation / Regulation of APC/C activators between G1/S and early anaphase / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / cyclin-dependent protein serine/threonine kinase activator activity / Condensation of Prometaphase Chromosomes / cyclin-dependent protein serine/threonine kinase regulator activity / mitotic metaphase chromosome alignment / positive regulation of G2/M transition of mitotic cell cycle / Cyclin A/B1/B2 associated events during G2/M transition / ubiquitin-like protein ligase binding / Nuclear events stimulated by ALK signaling in cancer / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Resolution of Sister Chromatid Cohesion / APC/C:Cdc20 mediated degradation of Cyclin B / positive regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / G2/M transition of mitotic cell cycle / spindle pole / positive regulation of fibroblast proliferation / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / in utero embryonic development / mitochondrial matrix / cell division / centrosome / protein kinase binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Brown, N.R. / Petri, E. / Lowe, E.D. / Skamnaki, V. / Johnson, L.N. | ||||||
Citation | Journal: Cell Cycle / Year: 2007 Title: Cyclin B and cyclin A confer different substrate recognition properties on CDK2. Authors: Brown, N.R. / Lowe, E.D. / Petri, E. / Skamnaki, V. / Antrobus, R. / Johnson, L.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jgz.cif.gz | 123.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jgz.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 2jgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jgz_validation.pdf.gz | 327.3 KB | Display | wwPDB validaton report |
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Full document | 2jgz_full_validation.pdf.gz | 329.2 KB | Display | |
Data in XML | 2jgz_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 2jgz_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/2jgz ftp://data.pdbj.org/pub/pdb/validation_reports/jg/2jgz | HTTPS FTP |
-Related structure data
Related structure data | 1qmzS S: Starting model for refinement |
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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: 32999.125 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-288 Source method: isolated from a genetically manipulated source Details: PHOSPHORYLATED ON THR160 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Protein | Mass: 30107.293 Da / Num. of mol.: 1 / Fragment: RESIDUES 167-426 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P14635 |
#3: Water | ChemComp-HOH / |
Sequence details | RESIDUE SER 0 DERIVES FROM THE EXPRESSION CONSTRUCT A FRAGMENT CONTAINING RESIDUES 165-433 WAS USED ...RESIDUE SER 0 DERIVES FROM THE EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.5 % |
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Crystal grow | pH: 6 Details: 0.9-1.2 M AMMONIUM SULPHATE, 100 MM MES PH 6.0-6.5, 100 MM POTASSIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8726 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30.18 Å / Num. obs: 19123 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QMZ Resolution: 2.9→29.64 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.864 / SU B: 15.137 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 2.771 / ESU R Free: 0.403 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.82 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→29.64 Å
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