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Yorodumi- PDB-8joy: Plk1 polo-box domain bound to HPV4 L2 residues 251-257 with pThr255 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8joy | ||||||
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Title | Plk1 polo-box domain bound to HPV4 L2 residues 251-257 with pThr255 | ||||||
Components |
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Keywords | CELL CYCLE / Plk1 / polo-box domain / PBD / HPV / L2 / HPV4 | ||||||
Function / homology | Function and homology information Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / nuclear membrane disassembly / polo kinase / mitotic nuclear membrane disassembly ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / nuclear membrane disassembly / polo kinase / mitotic nuclear membrane disassembly / protein localization to nuclear envelope / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / regulation of protein binding / anaphase-promoting complex binding / Phosphorylation of the APC/C / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / microtubule-dependent intracellular transport of viral material towards nucleus / regulation of mitotic spindle assembly / microtubule bundle formation / Polo-like kinase mediated events / mitotic chromosome condensation / Golgi Cisternae Pericentriolar Stack Reorganization / sister chromatid cohesion / regulation of mitotic metaphase/anaphase transition / centrosome cycle / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / positive regulation of proteolysis / centriolar satellite / mitotic cytokinesis / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / protein localization to chromatin / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / centriole / AURKA Activation by TPX2 / Condensation of Prophase Chromosomes / mitotic spindle organization / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / RHO GTPases Activate Formins / protein destabilization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / establishment of protein localization / kinetochore / spindle pole / positive regulation of protein localization to nucleus / spindle / viral penetration into host nucleus / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / viral capsid / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / host cell endosome / microtubule binding / host cell Golgi apparatus / peptidyl-serine phosphorylation / regulation of cell cycle / protein kinase activity / protein ubiquitination / symbiont entry into host cell / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / host cell nucleus / chromatin / negative regulation of apoptotic process / protein kinase binding / structural molecule activity / negative regulation of transcription by RNA polymerase II / magnesium ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human papillomavirus 4 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | ||||||
Authors | Ku, B. / Jung, S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: J.Microbiol / Year: 2023 Title: Crystal Structures of Plk1 Polo-Box Domain Bound to the Human Papillomavirus Minor Capsid Protein L2-Derived Peptide. Authors: Jung, S. / Lee, H.S. / Shin, H.C. / Choi, J.S. / Kim, S.J. / Ku, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8joy.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8joy.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 8joy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8joy_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 8joy_full_validation.pdf.gz | 438.7 KB | Display | |
Data in XML | 8joy_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 8joy_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/8joy ftp://data.pdbj.org/pub/pdb/validation_reports/jo/8joy | HTTPS FTP |
-Related structure data
Related structure data | 8joqC C: citing same article (ref.) |
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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
#1: Protein | Mass: 26165.857 Da / Num. of mol.: 1 / Fragment: polo-box domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Production host: Escherichia coli (E. coli) / References: UniProt: P53350, polo kinase |
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#2: Protein/peptide | Mass: 867.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: phosphoThr255 / Source: (synth.) Human papillomavirus 4 / References: UniProt: Q07862 |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M malate MES Tris buffer pH 6.5, 25% polyethylene glycol 1500 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 6436 / % possible obs: 95.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 48.53 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 5.19 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 0.503 / Num. unique obs: 315 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→39.65 Å / SU ML: 0.3112 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 28.3728 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.63 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.61→39.65 Å
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Refine LS restraints |
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LS refinement shell |
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