[English] 日本語
Yorodumi
- PDB-8joy: Plk1 polo-box domain bound to HPV4 L2 residues 251-257 with pThr255 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8joy
TitlePlk1 polo-box domain bound to HPV4 L2 residues 251-257 with pThr255
Components
  • Peptide from Minor capsid protein L2
  • Serine/threonine-protein kinase PLK1
KeywordsCELL 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 / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / mitotic nuclear membrane disassembly / polo kinase / protein localization to nuclear envelope / Phosphorylation of Emi1 ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / mitotic nuclear membrane disassembly / polo kinase / protein localization to nuclear envelope / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / nuclear membrane disassembly / synaptonemal complex / female meiosis chromosome segregation / Golgi inheritance / Phosphorylation of the APC/C / anaphase-promoting complex binding / outer kinetochore / positive regulation of ubiquitin protein ligase activity / microtubule bundle formation / double-strand break repair via alternative nonhomologous end joining / mitotic chromosome condensation / microtubule-dependent intracellular transport of viral material towards nucleus / Polo-like kinase mediated events / regulation of mitotic spindle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / centrosome cycle / regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin-protein transferase activity / sister chromatid cohesion / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / mitotic G2 DNA damage checkpoint signaling / regulation of anaphase-promoting complex-dependent catabolic process / mitotic cytokinesis / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / positive regulation of proteolysis / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin A/B1/B2 associated events during G2/M transition / protein localization to chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / centriole / 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 / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / Condensation of Prophase Chromosomes / regulation of cytokinesis / AURKA Activation by TPX2 / mitotic spindle organization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / establishment of protein localization / RHO GTPases Activate Formins / protein destabilization / kinetochore / centriolar satellite / positive regulation of protein localization to nucleus / spindle / viral penetration into host nucleus / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / spindle pole / Regulation of PLK1 Activity at G2/M Transition / G2/M transition of mitotic cell cycle / peptidyl-serine phosphorylation / viral capsid / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / mitotic cell cycle / host cell / microtubule cytoskeleton / midbody / host cell endosome / host cell Golgi apparatus / microtubule binding / protein ubiquitination / protein kinase activity / regulation of cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / symbiont entry into host cell / negative regulation of apoptotic process / protein kinase binding / chromatin / host cell nucleus / structural molecule activity / magnesium ion binding / negative regulation of transcription by RNA polymerase II / DNA binding
Similarity search - Function
Late protein L2 / Late Protein L2 / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site ...Late protein L2 / Late Protein L2 / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase PLK1 / Minor capsid protein L2
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus 4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsKu, B. / Jung, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019M3E5D6063955 Korea, Republic Of
CitationJournal: 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
DepositionJun 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: Peptide from Minor capsid protein L2


Theoretical massNumber of molelcules
Total (without water)27,0342
Polymers27,0342
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-7 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.106, 54.691, 57.578
Angle α, β, γ (deg.)90.000, 90.023, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Serine/threonine-protein kinase PLK1 / Polo-like kinase 1 / PLK-1 / Serine/threonine-protein kinase 13 / STPK13


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
#2: Protein/peptide Peptide from Minor capsid protein L2 / HPV4 L2 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 / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M malate MES Tris buffer pH 6.5, 25% polyethylene glycol 1500

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.503 / Num. unique obs: 315

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2546 630 9.82 %
Rwork0.1978 5786 -
obs0.2034 6416 94.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.63 Å2
Refinement stepCycle: LAST / Resolution: 2.61→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 0 17 1813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931834
X-RAY DIFFRACTIONf_angle_d1.17952484
X-RAY DIFFRACTIONf_chiral_restr0.0649278
X-RAY DIFFRACTIONf_plane_restr0.0067312
X-RAY DIFFRACTIONf_dihedral_angle_d12.85441108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.870.31341500.24541429X-RAY DIFFRACTION93.82
2.87-3.290.25921580.21721448X-RAY DIFFRACTION96.4
3.29-4.140.26461700.18721444X-RAY DIFFRACTION95.67
4.14-39.650.23161520.18651465X-RAY DIFFRACTION94.12

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more