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- PDB-9fjj: Two PLK1 PBD proteins bound to CENP-U(39-114) phosphorylated at T... -

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Basic information

Entry
Database: PDB / ID: 9fjj
TitleTwo PLK1 PBD proteins bound to CENP-U(39-114) phosphorylated at Thr78 and Thr98
Components
  • Centromere protein U
  • Serine/threonine-protein kinase PLK1
KeywordsCELL CYCLE / PLK1 PBD
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
DI(HYDROXYETHYL)ETHER / Serine/threonine-protein kinase PLK1 / Centromere protein U
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: Two PLK1 PBD proteins bound to CENP-U(39-114) phosphorylated at Thr78 and Thr98
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

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: Serine/threonine-protein kinase PLK1
U: Centromere protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8765
Polymers68,6783
Non-polymers1982
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-36 kcal/mol
Surface area24460 Å2
Unit cell
Length a, b, c (Å)83.790, 134.170, 60.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 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: 8665.939 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
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M tri-Lithium citrate, 20 v/v% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2→45.09 Å / Num. obs: 46806 / % possible obs: 99.2 % / Redundancy: 11.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.165 / Rrim(I) all: 0.174 / Net I/σ(I): 9.54
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2-2.052.27234140.4072.3821
2.05-2.111.8333320.6261.9181
2.11-2.171.3832180.6521.4471
2.17-2.241.13331410.7251.1871
2.24-2.310.94230370.8120.9881
2.31-2.390.83429680.8560.8741
2.39-2.480.7128590.8870.7441
2.48-2.580.54727600.9360.5741
2.58-2.70.49426440.9450.5181
2.7-2.830.40725490.9610.4271
2.83-2.980.31424310.9760.331
2.98-3.160.25522990.9850.2681
3.16-3.380.19821760.990.2081
3.38-3.650.15419990.9910.1631
3.65-40.12618600.9950.1331
4-4.470.10717080.9950.1131
4.47-5.160.09615220.9960.1011
5.16-6.320.09112920.9960.0961
6.32-8.940.08110250.9960.0851
8.94-45.090.0755720.9960.0791

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.09 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 2340 5 %
Rwork0.207 --
obs0.2087 46796 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 13 109 4140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064139
X-RAY DIFFRACTIONf_angle_d0.7765601
X-RAY DIFFRACTIONf_dihedral_angle_d17.5051546
X-RAY DIFFRACTIONf_chiral_restr0.047612
X-RAY DIFFRACTIONf_plane_restr0.007714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.37411360.3552575X-RAY DIFFRACTION99
2.04-2.090.36911350.30842572X-RAY DIFFRACTION99
2.09-2.130.33621340.29272541X-RAY DIFFRACTION99
2.13-2.190.28411370.25592595X-RAY DIFFRACTION99
2.19-2.250.28431350.23592578X-RAY DIFFRACTION99
2.25-2.310.26161360.2272582X-RAY DIFFRACTION99
2.31-2.390.27271370.23392599X-RAY DIFFRACTION99
2.39-2.470.29471360.2382591X-RAY DIFFRACTION99
2.47-2.570.32051370.24252593X-RAY DIFFRACTION99
2.57-2.690.29311380.23482621X-RAY DIFFRACTION99
2.69-2.830.28951370.23092608X-RAY DIFFRACTION100
2.83-3.010.24021380.21842618X-RAY DIFFRACTION100
3.01-3.240.2581390.22752648X-RAY DIFFRACTION100
3.24-3.560.26481380.21312626X-RAY DIFFRACTION99
3.57-4.080.23151390.18842631X-RAY DIFFRACTION99
4.08-5.140.17111420.15972701X-RAY DIFFRACTION100
5.14-45.090.2061460.18332777X-RAY DIFFRACTION98

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