[English] 日本語
Yorodumi
- PDB-8s30: Crystal structure of human PLK1 Polo-Box Domain in complex with Mis18 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8s30
TitleCrystal structure of human PLK1 Polo-Box Domain in complex with Mis18
Components
  • Protein Mis18-alpha
  • Serine/threonine-protein kinase PLK1
KeywordsCELL CYCLE / PLK1 / Mis18 complex / Centromere / Chromosome missegregation
Function / homology
Function and homology information


regulation of anaphase-promoting complex-dependent catabolic process / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / nuclear membrane disassembly / regulation of protein binding ...regulation of anaphase-promoting complex-dependent catabolic process / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / nuclear membrane disassembly / regulation of protein binding / polo kinase / mitotic nuclear membrane disassembly / protein localization to nuclear envelope / CENP-A containing chromatin assembly / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / anaphase-promoting complex binding / outer kinetochore / Phosphorylation of the APC/C / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / regulation of mitotic spindle assembly / microtubule bundle formation / Polo-like kinase mediated events / mitotic chromosome condensation / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / sister chromatid cohesion / centrosome cycle / regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic cell cycle phase transition / double-strand break repair via alternative nonhomologous end joining / mitotic spindle assembly checkpoint signaling / Cyclin A/B1/B2 associated events during G2/M transition / mitotic spindle pole / regulation of mitotic cell cycle / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / mitotic G2 DNA damage checkpoint signaling / positive regulation of proteolysis / mitotic cytokinesis / chromosome, centromeric region / centriolar satellite / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deposition of new CENPA-containing nucleosomes at the centromere / 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 / Resolution of Sister Chromatid Cohesion / centriole / AURKA Activation by TPX2 / Condensation of Prophase Chromosomes / mitotic spindle organization / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / chromosome segregation / 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 / G2/M transition of mitotic cell cycle / spindle pole / positive regulation of protein localization to nucleus / spindle / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / peptidyl-serine phosphorylation / midbody / microtubule binding / regulation of cell cycle / protein kinase activity / protein ubiquitination / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / chromatin / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / ATP binding
Similarity search - Function
Mis18 domain / Mis18 domain profile. / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / 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 ...Mis18 domain / Mis18 domain profile. / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / 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. / Serine/Threonine protein kinases, catalytic domain / Protein kinase 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 / Protein Mis18-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsJeyaprakash, A.A. / Medina-Pritchard, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/X001245/1 United Kingdom
CitationJournal: Science / Year: 2024
Title: PLK1-mediated phosphorylation cascade activates Mis18 complex to ensure centromere inheritance
Authors: Jeyaprakash, A.A. / Medina-Pritchard, B.
History
DepositionFeb 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: Protein Mis18-alpha


Theoretical massNumber of molelcules
Total (without water)28,7572
Polymers28,7572
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-9 kcal/mol
Surface area10760 Å2
Unit cell
Length a, b, c (Å)43.138, 56.568, 49.576
Angle α, β, γ (deg.)90.000, 115.740, 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: 27877.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Plasmid: pEC-A-HT_SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P53350, polo kinase
#2: Protein/peptide Protein Mis18-alpha / FAPP1-associated protein 1


Mass: 878.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NYP9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 35.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.09 M Halogen mix (NaF, NaBr, NaI), 0.1 M buffer system 2 (Sodium HEPES and MOPS) (pH7.5), 37% precipitant mix MPD_P1K_P3350 (MPD (racemic), PEG 1K, PEG 3350)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979499 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979499 Å / Relative weight: 1
ReflectionResolution: 1.94→44.66 Å / Num. obs: 15410 / % possible obs: 94.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.66 Å2 / CC1/2: 0.978 / CC star: 0.995 / Net I/σ(I): 7.16
Reflection shellResolution: 1.94→2.009 Å / Rmerge(I) obs: 0.8879 / Num. unique obs: 1116 / CC1/2: 0.271

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→44.66 Å / SU ML: 0.2953 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.0404
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2707 740 4.88 %
Rwork0.2169 14437 -
obs0.2194 15177 94.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.5 Å2
Refinement stepCycle: LAST / Resolution: 1.94→44.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 0 85 1833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081783
X-RAY DIFFRACTIONf_angle_d1.09722407
X-RAY DIFFRACTIONf_chiral_restr0.0575268
X-RAY DIFFRACTIONf_plane_restr0.0111297
X-RAY DIFFRACTIONf_dihedral_angle_d7.5602241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.090.33741340.2852159X-RAY DIFFRACTION71.37
2.09-2.290.2871650.24323010X-RAY DIFFRACTION98.88
2.29-2.630.26771340.22853067X-RAY DIFFRACTION99.94
2.63-3.310.26821550.23083082X-RAY DIFFRACTION99.97
3.31-44.660.25951520.19453119X-RAY DIFFRACTION99.82
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)
13.606310002330.03464699419050.3853370184923.79173373569-4.089988047974.46054557984-0.00529952439683-0.6467429301740.5745285735321.508511693190.0512056527964-0.427252417134-1.020381624050.331227350223-0.006808033528760.428133830448-0.110548479886-0.0002812626410710.34534297447-0.06645806819420.21647803858212.778909680522.291836245421.4513679529
22.409408886170.796198286533-0.7965172950561.16810500633-0.4390596543410.995229392867-0.02953333866720.0536189265458-0.0434404488268-0.0337307914258-0.01896431111980.03672928277760.0832081822721-0.02122730789830.0771722346940.2770879760970.0158180564358-0.02020337542810.242673346901-0.01533408431230.2832862338144.7237700284810.418271257113.0977734554
33.064831210540.09723641327651.108005034491.511307967120.1871440097923.73920778794-0.05137527100320.317987663967-0.145746463063-0.119675222219-0.000427269176619-0.2080028500810.06731010689370.1633657612860.03745445233720.2565683056610.0454520323981-0.01777148325560.330349924692-0.05385465204470.39497911735618.652552164214.46984778346.61596466697
41.786645154850.820669891826-0.1960003997293.3505340812-1.012667182791.316473779810.02035418828730.05234577274980.006060481371940.0315418787785-0.07268521249110.195231121057-0.003824953301560.04484983332880.0503076417090.1821194887870.0318408809823-0.01940960922680.230036274796-0.01789008985790.237575457576-1.9290298472711.704176537718.7628040037
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 0 through 5 )BB0 - 51 - 6
22chain 'A' and (resid 373 through 454 )AA373 - 4541 - 82
33chain 'A' and (resid 455 through 510 )AA455 - 51083 - 127
44chain 'A' and (resid 511 through 592 )AA511 - 592128 - 209

+
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://pdbjlc1.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