[English] 日本語
Yorodumi
- PDB-6gy2: Crystal structure of human Plk1-PBD in complex with WSSSLATPPTLSS... -

+
Open data


ID or keywords:

Loading...

-
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 Telophase/Cytokinesis / regulation of protein localization to cell cortex / mitotic recombination-dependent replication fork processing / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / establishment of protein localization to telomere / regulation of protein binding ...BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / mitotic recombination-dependent replication fork processing / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / establishment of protein localization to telomere / regulation of protein binding / Activation of NIMA Kinases NEK9, NEK6, NEK7 / nuclear membrane disassembly / homologous chromosome segregation / polo kinase / mitotic nuclear membrane disassembly / Phosphorylation of Emi1 / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / protein localization to nuclear envelope / nuclear ubiquitin ligase complex / metaphase/anaphase transition of mitotic cell cycle / double-strand break repair via alternative nonhomologous end joining / synaptonemal complex / female meiosis chromosome segregation / anaphase-promoting complex binding / Phosphorylation of the APC/C / lateral element / telomere maintenance via recombination / histone H4 acetyltransferase activity / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / histone H3 acetyltransferase activity / regulation of DNA damage checkpoint / regulation of mitotic spindle assembly / positive regulation of ubiquitin protein ligase activity / Impaired BRCA2 binding to PALB2 / microtubule bundle formation / HDR through MMEJ (alt-NHEJ) / gamma-tubulin binding / mitotic chromosome condensation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / response to UV-C / DNA repair complex / centrosome cycle / regulation of mitotic metaphase/anaphase transition / Homologous DNA Pairing and Strand Exchange / 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 / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / positive regulation of ubiquitin-protein transferase activity / oocyte maturation / sister chromatid cohesion / Resolution of D-loop Structures through Holliday Junction Intermediates / inner cell mass cell proliferation / regulation of mitotic cell cycle phase transition / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / hematopoietic stem cell proliferation / Impaired BRCA2 binding to RAD51 / female gonad development / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / male meiosis I / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / establishment of mitotic spindle orientation / positive regulation of proteolysis / mitotic sister chromatid segregation / Presynaptic phase of homologous DNA pairing and strand exchange / centrosome duplication / mitotic cytokinesis / centriolar satellite / response to X-ray / negative regulation of double-strand break repair via homologous recombination / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / spindle midzone / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / 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 / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / centriole / AURKA Activation by TPX2 / positive regulation of mitotic cell cycle / mitotic spindle organization / Condensation of Prophase Chromosomes / regulation of cytokinesis / secretory granule / positive regulation of peptidyl-threonine phosphorylation / response to gamma radiation / cellular response to ionizing radiation
Similarity search - Function
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 / BRCA2, OB2 / BRCA2 TR2 domain ...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 / BRCA2, OB2 / BRCA2 TR2 domain / 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 / Serine/Threonine protein kinases, catalytic domain / Nucleic acid-binding, OB-fold / 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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