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- PDB-8joy: Plk1 polo-box domain bound to HPV4 L2 residues 251-257 with pThr255 -

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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 / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / homologous chromosome segregation / protein localization to nuclear envelope / polo kinase ...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 / mitotic nuclear membrane disassembly / homologous chromosome segregation / protein localization to nuclear envelope / polo kinase / nuclear membrane disassembly / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / Phosphorylation of the APC/C / anaphase-promoting complex binding / regulation of protein binding / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / double-strand break repair via alternative nonhomologous end joining / 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 / Golgi Cisternae Pericentriolar Stack Reorganization / mitotic chromosome condensation / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / positive regulation of ubiquitin-protein transferase activity / centrosome cycle / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic sister chromatid segregation / mitotic G2 DNA damage checkpoint signaling / positive regulation of proteolysis / establishment of mitotic spindle orientation / mitotic cytokinesis / centriolar satellite / spindle midzone / 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 / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / regulation of mitotic cell cycle / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / mitotic spindle organization / Condensation of Prophase Chromosomes / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / 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 / spindle pole / positive regulation of protein localization to nucleus / viral penetration into host nucleus / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / viral capsid / Regulation of PLK1 Activity at G2/M Transition / 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 / protein ubiquitination / regulation of cell cycle / protein kinase activity / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Water


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

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Experimental details

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Experiment

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

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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

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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

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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

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