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Yorodumi- PDB-1f5q: CRYSTAL STRUCTURE OF MURINE GAMMA HERPESVIRUS CYCLIN COMPLEXED TO... -
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-Basic information
Entry | Database: PDB / ID: 1f5q | ||||||
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Title | CRYSTAL STRUCTURE OF MURINE GAMMA HERPESVIRUS CYCLIN COMPLEXED TO HUMAN CYCLIN DEPENDENT KINASE 2 | ||||||
Components |
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Keywords | TRANSFERASE / herpesviral cyclin / cyclin dependent kinase. protein-protein complex | ||||||
Function / homology | Function and homology information cyclin-dependent protein serine/threonine kinase regulator activity / 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 ...cyclin-dependent protein serine/threonine kinase regulator activity / 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 / 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 maintenance in response to DNA damage / G0 and Early G1 / Telomere Extension By Telomerase / cellular response to nitric oxide / Activation of the pre-replicative complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / 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-dependent protein kinase holoenzyme complex / mitotic G1 DNA damage checkpoint signaling / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / post-translational protein modification / cyclin binding / positive regulation of DNA replication / male germ cell nucleus / meiotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / peptidyl-serine phosphorylation / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / DNA replication / chromosome, telomeric region / endosome / chromatin remodeling / protein phosphorylation / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Murid herpesvirus 4 (Murine herpesvirus 68) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Card, G.L. / Knowles, P. / Laman, H. / Jones, N. / McDonald, N.Q. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: Crystal structure of a gamma-herpesvirus cyclin-cdk complex. Authors: Card, G.L. / Knowles, P. / Laman, H. / Jones, N. / McDonald, N.Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f5q.cif.gz | 220.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f5q.ent.gz | 178.1 KB | Display | PDB format |
PDBx/mmJSON format | 1f5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f5q_validation.pdf.gz | 390.6 KB | Display | wwPDB validaton report |
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Full document | 1f5q_full_validation.pdf.gz | 428.2 KB | Display | |
Data in XML | 1f5q_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 1f5q_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/1f5q ftp://data.pdbj.org/pub/pdb/validation_reports/f5/1f5q | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33976.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 INSECT CELLS / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Protein | Mass: 29067.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68) Genus: Rhadinovirus / Plasmid: PGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P89883 #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
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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: 2.68 Å3/Da / Density % sol: 54.17 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES, 12% propan-2-ol, 5% PEG 4K, 10mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.7817 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 24, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7817 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 45057 / Num. obs: 140317 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 48.48 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.5→30 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.379 / Num. unique all: 6394 / % possible all: 95.6 |
Reflection | *PLUS Num. obs: 45057 / Num. measured all: 140317 |
Reflection shell | *PLUS % possible obs: 95.6 % / Mean I/σ(I) obs: 1.6 |
-Processing
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Refinement | Resolution: 2.5→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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