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- PDB-6gy2: Crystal structure of human Plk1-PBD in complex with WSSSLATPPTLSS... -

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Basic information

Entry
Database: PDB / ID: 6gy2
TitleCrystal structure of human Plk1-PBD in complex with WSSSLATPPTLSSpTVLI phosphopeptide from BRCA2
Components
  • Phosphopeptide of BRCA2
  • Serine/threonine-protein kinase PLK1
KeywordsCELL CYCLE / phosphorylation / chromosomes alignement / DNA repair
Function / homology
Function and homology information


BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / establishment of protein localization to telomere / mitotic nuclear membrane disassembly ...BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / establishment of protein localization to telomere / mitotic nuclear membrane disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / protein localization to nuclear envelope / polo kinase / nuclear membrane disassembly / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / Phosphorylation of Emi1 / nuclear ubiquitin ligase complex / metaphase/anaphase transition of mitotic cell cycle / histone H3 acetyltransferase activity / histone H4 acetyltransferase activity / synaptonemal complex / female meiosis chromosome segregation / lateral element / telomere maintenance via recombination / outer kinetochore / Phosphorylation of the APC/C / anaphase-promoting complex binding / regulation of protein binding / regulation of DNA damage checkpoint / double-strand break repair via alternative nonhomologous end joining / negative regulation of cyclin-dependent protein serine/threonine kinase activity / HDR through MMEJ (alt-NHEJ) / positive regulation of ubiquitin protein ligase activity / oocyte maturation / Impaired BRCA2 binding to PALB2 / regulation of mitotic spindle assembly / microtubule bundle formation / gamma-tubulin binding / Polo-like kinase mediated events / mitotic chromosome condensation / Golgi Cisternae Pericentriolar Stack Reorganization / DNA repair complex / positive regulation of ubiquitin-protein transferase activity / sister chromatid cohesion / regulation of mitotic metaphase/anaphase transition / centrosome cycle / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / response to UV-C / Resolution of D-loop Structures through Holliday Junction Intermediates / regulation of mitotic cell cycle phase transition / inner cell mass cell proliferation / Impaired BRCA2 binding to RAD51 / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / hematopoietic stem cell proliferation / female gonad development / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / male meiosis I / regulation of mitotic cell cycle / mitotic sister chromatid segregation / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / positive regulation of proteolysis / establishment of mitotic spindle orientation / Presynaptic phase of homologous DNA pairing and strand exchange / centrosome duplication / mitotic cytokinesis / centriolar satellite / response to X-ray / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 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 / Anchoring of the basal body to the plasma membrane / centriole / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / mitotic spindle organization / Condensation of Prophase Chromosomes / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / secretory granule / RHO GTPases Activate Formins / cellular response to ionizing radiation / nucleotide-excision repair / response to gamma radiation
Similarity search - Function
: / BRCA2, OB2 / BRCA2, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 / Tower / BRCA2, helical / Tower ...: / BRCA2, OB2 / BRCA2, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 / Tower / BRCA2, helical / Tower / BRCA2 repeat / BRCA2, OB1 / Breast cancer type 2 susceptibility protein / BRCA2 repeat / BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 / BRCA2 repeat profile. / POLO box domain / 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. / Arylsulfatase, C-terminal domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Nucleic acid-binding, OB-fold / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Breast cancer type 2 susceptibility protein / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsMiron, S. / Ropars, V. / Zinn-Justin, S.
Funding support France, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)INCa-DGOS_8706 France
CitationJournal: Nat Commun / Year: 2020
Title: Proper chromosome alignment depends on BRCA2 phosphorylation by PLK1.
Authors: Ehlen, A. / Martin, C. / Miron, S. / Julien, M. / Theillet, F.X. / Ropars, V. / Sessa, G. / Beaurepere, R. / Boucherit, V. / Duchambon, P. / El Marjou, A. / Zinn-Justin, S. / Carreira, A.
History
DepositionJun 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 30, 2022Group: Advisory / Author supporting evidence / Database references
Category: database_2 / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: Serine/threonine-protein kinase PLK1
C: Phosphopeptide of BRCA2
D: Phosphopeptide of BRCA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1585
Polymers60,0664
Non-polymers921
Water39622
1
A: Serine/threonine-protein kinase PLK1
D: Phosphopeptide of BRCA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1253
Polymers30,0332
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-11 kcal/mol
Surface area12100 Å2
MethodPISA
2
B: Serine/threonine-protein kinase PLK1
C: Phosphopeptide of BRCA2


Theoretical massNumber of molelcules
Total (without water)30,0332
Polymers30,0332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-10 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.000, 56.040, 61.030
Angle α, β, γ (deg.)80.790, 79.230, 65.050
Int Tables number1
Space group name H-MP1

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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: 28193.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: the six first residues AMDPEF are part of LINKER / Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53350, polo kinase
#2: Protein/peptide Phosphopeptide of BRCA2


Mass: 1839.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P51587*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350, BisTris, DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.106→22.57 Å / Num. obs: 9934 / % possible obs: 93.7 % / Redundancy: 1.94 % / Biso Wilson estimate: 76.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.051 / Rrim(I) all: 0.076 / Net I/σ(I): 10.1
Reflection shellResolution: 3.106→3.16 Å / Redundancy: 1.98 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 523 / CC1/2: 0.821 / Rpim(I) all: 0.31 / Rrim(I) all: 0.466 / % possible all: 96.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O9W

4o9w


Resolution: 3.11→22.57 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.897 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.405
RfactorNum. reflection% reflectionSelection details
Rfree0.215 473 4.77 %RANDOM
Rwork0.187 ---
obs0.189 9911 93.7 %-
Displacement parametersBiso max: 169 Å2 / Biso mean: 78.86 Å2 / Biso min: 34 Å2
Baniso -1Baniso -2Baniso -3
1--27.2101 Å2-10.0131 Å2-8.8733 Å2
2--14.3071 Å2-2.6857 Å2
3---12.9029 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 3.11→22.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 6 22 3842
Biso mean--85.33 57.56 -
Num. residues----472
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1372SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes647HARMONIC5
X-RAY DIFFRACTIONt_it3897HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion503SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4259SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3897HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg5277HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion18.58
LS refinement shellResolution: 3.11→3.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 23
RfactorNum. reflection% reflection
Rfree0.2345 22 5.1 %
Rwork0.2435 409 -
all0.243 431 -
obs--96.24 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5103-1.7691-1.24674.01250.5371.9666-0.0463-0.13460.0360.09360.0078-0.075-0.11880.02330.0385-0.0904-0.1401-0.0105-0.06590.0189-0.0953-0.0228-14.03152.3126
22.4771-1.46030.60023.7121-0.30371.7841-0.0607-0.1870.03360.1193-0.0136-0.08970.032-0.05190.0744-0.0652-0.12740.0674-0.0410.0483-0.1173-19.4783-24.412428.8895
3-0.00270.01910.08180.23210.73880.8595-0.0013-0.00210.0169-0.0030.00190.01480.0033-0.0113-0.00060.0004-0.03690.01750.06-0.0538-0.0316-28.5106-24.881413.1956
4-0.0340.0689-0.1290.2047-0.07531.1825-0.00040.0044-0.02950.00290.00720.0094-0.01260.0105-0.00680.0132-0.01650.04410.0403-0.0128-0.0412.4456-16.7815-15.2253
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A370 - 593
2X-RAY DIFFRACTION2{ B|* }B371 - 594
3X-RAY DIFFRACTION3{ C|* }C199 - 210
4X-RAY DIFFRACTION4{ D|* }D199 - 210

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