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- PDB-9fjh: Two PLK1 PBD proteins bound to CENP-U(58-114) phosphorylated at T... -

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Basic information

Entry
Database: PDB / ID: 9fjh
TitleTwo PLK1 PBD proteins bound to CENP-U(58-114) phosphorylated at Thr78 and Thr98
Components
  • Centromere protein U
  • Serine/threonine-protein kinase PLK1
KeywordsCELL CYCLE / PLK1 / CCAN / kinase / mitosis / kinetochore / CENP-U / phosphorylation
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / polo kinase / mitotic nuclear membrane disassembly / homologous chromosome segregation / protein localization to nuclear envelope / Phosphorylation of Emi1 ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / polo kinase / mitotic nuclear membrane disassembly / homologous chromosome segregation / protein localization to nuclear envelope / Phosphorylation of Emi1 / chordate embryonic development / metaphase/anaphase transition of mitotic cell cycle / female meiosis chromosome segregation / nuclear membrane disassembly / synaptonemal complex / Phosphorylation of the APC/C / anaphase-promoting complex binding / Golgi inheritance / outer kinetochore / positive regulation of ubiquitin protein ligase activity / inner kinetochore / microtubule bundle formation / double-strand break repair via alternative nonhomologous end joining / mitotic chromosome condensation / Polo-like kinase mediated events / regulation of mitotic spindle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / centrosome cycle / regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin-protein transferase activity / sister chromatid cohesion / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / spindle midzone / mitotic G2 DNA damage checkpoint signaling / regulation of anaphase-promoting complex-dependent catabolic process / mitotic cytokinesis / positive regulation of proteolysis / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / negative regulation of double-strand break repair via homologous recombination / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin A/B1/B2 associated events during G2/M transition / protein localization to chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / Deposition of new CENPA-containing nucleosomes at the centromere / centriole / 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 / 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 / Condensation of Prophase Chromosomes / AURKA Activation by TPX2 / regulation of cytokinesis / mitotic spindle organization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / chromosome segregation / establishment of protein localization / RHO GTPases Activate Formins / protein destabilization / peptidyl-serine phosphorylation / kinetochore / positive regulation of protein localization to nucleus / centriolar satellite / G2/M transition of mitotic cell cycle / spindle / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / spindle pole / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / mitotic cell cycle / microtubule cytoskeleton / midbody / microtubule binding / protein phosphorylation / protein kinase activity / protein ubiquitination / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / negative regulation of apoptotic process / chromatin / magnesium ion binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Centromere protein U / CENP-A nucleosome associated complex (NAC) subunit / 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 ...Centromere protein U / CENP-A nucleosome associated complex (NAC) subunit / 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
TRIETHYLENE GLYCOL / PHOSPHATE ION / Serine/threonine-protein kinase PLK1 / Centromere protein U
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRen, L. / Gasper, R. / Vetter, I.R. / Musacchio, A.
Funding supportEuropean Union, Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)951430European Union
German Research Foundation (DFG)1430 Germany
CitationJournal: To be published
Title: Structural and molecular basis of kinaseregulated inner-kinetochore recruitment of PLK1 by CENP-U
Authors: Ren, L. / Gasper, R. / Vetter, I.R. / Musacchio, A.
History
DepositionMay 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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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: Serine/threonine-protein kinase PLK1
C: Centromere protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1767
Polymers66,5863
Non-polymers5904
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-31 kcal/mol
Surface area23540 Å2
Unit cell
Length a, b, c (Å)84.890, 135.090, 60.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein Serine/threonine-protein kinase PLK1 / Polo-like kinase 1 / PLK-1 / Serine/threonine-protein kinase 13 / STPK13


Mass: 30006.166 Da / Num. of mol.: 2
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 Centromere protein U / CENP-U / Centromere protein of 50 kDa / CENP-50 / Interphase centromere complex protein 24 / KSHV ...CENP-U / Centromere protein of 50 kDa / CENP-50 / Interphase centromere complex protein 24 / KSHV latent nuclear antigen-interacting protein 1 / MLF1-interacting protein / Polo-box-interacting protein 1


Mass: 6573.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPU, ICEN24, KLIP1, MLF1IP, PBIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q71F23

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Non-polymers , 4 types, 56 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.2M NaCl, 0.1 M CHES pH9.5, 10 v/v% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99984166392118 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984166392118 Å / Relative weight: 1
ReflectionResolution: 2.15→42.45 Å / Num. obs: 38912 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.085 / Net I/σ(I): 16.84
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.15-2.210.08228100.5710.16851
2.21-2.271.43827960.7251.4931
2.27-2.331.14626840.7591.191
2.33-2.40.8626070.8690.8931
2.4-2.480.68225180.9030.7091
2.48-2.570.524780.9440.5221
2.57-2.670.37623670.9690.3921
2.67-2.780.28822910.9820.2991
2.78-2.90.21322120.9920.2211
2.9-3.040.16521100.9940.1711
3.04-3.210.1219870.9970.1241
3.21-3.40.09119290.9980.0941
3.4-3.630.07417820.9980.0771
3.63-3.930.06216660.9990.0651
3.93-4.30.05415570.9990.0561
4.3-4.810.04814190.9990.051
4.81-5.550.04712610.9990.0491
5.55-6.80.0510750.9990.0521
6.8-9.620.0438570.9990.0441
9.62-36.220.0395060.9990.0411

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→42.45 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 1945 5 %
Rwork0.2163 --
obs0.218 38901 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3933 0 38 52 4023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024107
X-RAY DIFFRACTIONf_angle_d0.4885554
X-RAY DIFFRACTIONf_dihedral_angle_d16.7181551
X-RAY DIFFRACTIONf_chiral_restr0.039603
X-RAY DIFFRACTIONf_plane_restr0.004705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.34561360.33422587X-RAY DIFFRACTION100
2.2-2.260.35721370.2932604X-RAY DIFFRACTION100
2.26-2.330.31051370.27872595X-RAY DIFFRACTION100
2.33-2.410.32631370.26912606X-RAY DIFFRACTION100
2.41-2.490.31791370.27412611X-RAY DIFFRACTION100
2.49-2.590.31781370.28092596X-RAY DIFFRACTION100
2.59-2.710.31571380.26642624X-RAY DIFFRACTION100
2.71-2.850.27641390.24982627X-RAY DIFFRACTION100
2.85-3.030.30091380.26622625X-RAY DIFFRACTION100
3.03-3.260.31381380.27742627X-RAY DIFFRACTION100
3.26-3.590.28571400.23042666X-RAY DIFFRACTION100
3.59-4.110.22121410.1932668X-RAY DIFFRACTION100
4.11-5.180.16911420.14952696X-RAY DIFFRACTION100
5.18-42.450.23141480.19882824X-RAY DIFFRACTION100

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