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- PDB-8x72: The Crystal Structure of PLK1 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8x72
TitleThe Crystal Structure of PLK1 from Biortus.
ComponentsSerine/threonine-protein kinase PLK1
KeywordsTRANSFERASE / Kinase Cell cycle
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / polo kinase / nuclear membrane disassembly / mitotic nuclear membrane disassembly ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / polo kinase / nuclear membrane disassembly / mitotic nuclear membrane disassembly / protein localization to nuclear envelope / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / Phosphorylation of the APC/C / regulation of protein binding / anaphase-promoting complex binding / outer kinetochore / 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 / Golgi Cisternae Pericentriolar Stack Reorganization / mitotic chromosome condensation / sister chromatid cohesion / regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin-protein transferase activity / centrosome cycle / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / positive regulation of proteolysis / centriolar satellite / mitotic cytokinesis / spindle midzone / negative regulation of double-strand break repair via homologous recombination / 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 / regulation of mitotic cell cycle / centriole / AURKA Activation by TPX2 / Condensation of Prophase Chromosomes / mitotic spindle organization / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / 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 / spindle pole / positive regulation of protein localization to nucleus / spindle / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / 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 / midbody / microtubule binding / peptidyl-serine phosphorylation / regulation of cell cycle / protein kinase activity / protein ubiquitination / protein phosphorylation / 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 / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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
ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DI(HYDROXYETHYL)ETHER / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Wu, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of PLK1 from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Wu, B.
History
DepositionNov 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,56910
Polymers37,4811
Non-polymers1,0889
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-18 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.500, 67.500, 153.347
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine/threonine-protein kinase PLK1


Mass: 37480.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1 / Production host: Escherichia coli (E. coli) / References: UniProt: P53350

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Non-polymers , 6 types, 186 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.5M MgAc2, 12% PEG 4000, 0.3mM ZnAc2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 2.2→46.53 Å / Num. obs: 20455 / % possible obs: 96.2 % / Redundancy: 11 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 12.5
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 1.003 / Num. unique obs: 1737

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.53 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.179 / SU B: 7.279 / SU ML: 0.173 / Average fsc free: 0.8839 / Average fsc work: 0.897 / Cross valid method: FREE R-VALUE / ESU R: 0.239 / ESU R Free: 0.208
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2497 963 4.719 %
Rwork0.195 19445 -
all0.198 --
obs-20408 95.947 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.856 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20.765 Å20 Å2
2--1.53 Å2-0 Å2
3----4.964 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 66 177 2622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132497
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172442
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.6623361
X-RAY DIFFRACTIONr_angle_other_deg1.0991.5795629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5195293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.84220.227132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5515449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.731523
X-RAY DIFFRACTIONr_chiral_restr0.0520.2316
X-RAY DIFFRACTIONr_chiral_restr_other0.1290.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
X-RAY DIFFRACTIONr_nbd_refined0.1880.2450
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.22159
X-RAY DIFFRACTIONr_nbtor_refined0.1570.21181
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.21199
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2138
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2650.27
X-RAY DIFFRACTIONr_nbd_other0.2090.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0870.26
X-RAY DIFFRACTIONr_mcbond_it2.1464.7351177
X-RAY DIFFRACTIONr_mcbond_other2.1424.7311174
X-RAY DIFFRACTIONr_mcangle_it3.457.0911467
X-RAY DIFFRACTIONr_mcangle_other3.4497.0961468
X-RAY DIFFRACTIONr_scbond_it2.4585.1171320
X-RAY DIFFRACTIONr_scbond_other2.4585.1191321
X-RAY DIFFRACTIONr_scangle_it4.0817.5191894
X-RAY DIFFRACTIONr_scangle_other4.087.5221895
X-RAY DIFFRACTIONr_lrange_it6.03654.2232689
X-RAY DIFFRACTIONr_lrange_other6.01554.0782667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.339660.3051400X-RAY DIFFRACTION94.6417
2.257-2.3190.356660.2761399X-RAY DIFFRACTION97.3422
2.319-2.3860.267550.2561345X-RAY DIFFRACTION97.2898
2.386-2.4590.298840.2381281X-RAY DIFFRACTION95.9916
2.459-2.540.414480.2341293X-RAY DIFFRACTION96.129
2.54-2.6290.332580.221205X-RAY DIFFRACTION96.1919
2.629-2.7280.286490.2141202X-RAY DIFFRACTION96.7517
2.728-2.8390.283600.1961166X-RAY DIFFRACTION96.5354
2.839-2.9650.26590.1981087X-RAY DIFFRACTION96.3835
2.965-3.1090.28640.1911051X-RAY DIFFRACTION97.0409
3.109-3.2770.262540.2011005X-RAY DIFFRACTION97.0669
3.277-3.4750.297500.196961X-RAY DIFFRACTION97.3051
3.475-3.7140.25410.196928X-RAY DIFFRACTION97.2892
3.714-4.010.229540.177836X-RAY DIFFRACTION96.6341
4.01-4.3910.162390.143766X-RAY DIFFRACTION96.4072
4.391-4.9060.181320.149714X-RAY DIFFRACTION94.7903
4.906-5.6580.203310.182628X-RAY DIFFRACTION93.7411
5.658-6.9130.24220.203523X-RAY DIFFRACTION92.0608
6.913-9.7090.205180.17414X-RAY DIFFRACTION88.8889
9.709-46.530.232130.213241X-RAY DIFFRACTION85.8108

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