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- PDB-8joq: Plk1 polo-box domain bound to HPV18 L2 residues 209-215 with pThr213 -

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Basic information

Entry
Database: PDB / ID: 8joq
TitlePlk1 polo-box domain bound to HPV18 L2 residues 209-215 with pThr213
Components
  • HPV18 L2 peptide
  • Serine/threonine-protein kinase PLK1
KeywordsCELL CYCLE / Plk1 / polo-box domain / PBD / HPV / L2 / HPV18 / REPLICATION
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
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
Minor capsid protein L2 / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
human papillomavirus 18
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 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 8, 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: HPV18 L2 peptide


Theoretical massNumber of molelcules
Total (without water)26,9602
Polymers26,9602
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-9 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.143, 54.346, 57.295
Angle α, β, γ (deg.)90.00, 90.61, 90.00
Int Tables number4
Space group name H-MP1211

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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 HPV18 L2 peptide


Mass: 793.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) human papillomavirus 18 / References: UniProt: P06793
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
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: 5C (4A) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.796→50 Å / Num. obs: 18536 / % possible obs: 91.8 % / Redundancy: 3.8 % / Rsym value: 0.045 / Net I/σ(I): 5.5
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 958 / Rsym value: 0.199

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.796→35.141 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 1867 10.08 %
Rwork0.2056 --
obs0.21 18520 91.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.796→35.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 0 117 1942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071864
X-RAY DIFFRACTIONf_angle_d0.8912522
X-RAY DIFFRACTIONf_dihedral_angle_d19.7441131
X-RAY DIFFRACTIONf_chiral_restr0.056281
X-RAY DIFFRACTIONf_plane_restr0.006317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7961-1.84470.34151480.24281312X-RAY DIFFRACTION94
1.8447-1.8990.2971450.24371262X-RAY DIFFRACTION93
1.899-1.96020.33371050.25241013X-RAY DIFFRACTION71
1.9602-2.03030.30621420.23071359X-RAY DIFFRACTION98
2.0303-2.11160.27631590.23251374X-RAY DIFFRACTION99
2.1116-2.20770.25451650.21811376X-RAY DIFFRACTION99
2.2077-2.3240.27061100.2154833X-RAY DIFFRACTION61
2.324-2.46960.25481630.2311381X-RAY DIFFRACTION99
2.4696-2.66020.261410.22631383X-RAY DIFFRACTION99
2.6602-2.92780.25061600.22571410X-RAY DIFFRACTION99
2.9278-3.35120.25431480.20991390X-RAY DIFFRACTION99
3.3512-4.2210.21671260.18321127X-RAY DIFFRACTION79
4.221-35.1410.21491550.16241433X-RAY DIFFRACTION99

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