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- PDB-4rcp: Crystal structure of Plk1 Polo-box domain in complex with PL-2 -

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Basic information

Entry
Database: PDB / ID: 4rcp
TitleCrystal structure of Plk1 Polo-box domain in complex with PL-2
Components
  • PL-2
  • Serine/threonine-protein kinase PLK1
KeywordsTransferase/transferase inhibitor / Polo-box domain / Transferase-transferase inhibitor complex
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 / nuclear membrane disassembly / polo kinase / 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 / nuclear membrane disassembly / polo kinase / 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 / regulation of protein binding / anaphase-promoting complex binding / Phosphorylation of the APC/C / 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 / mitotic chromosome condensation / Golgi Cisternae Pericentriolar Stack Reorganization / sister chromatid cohesion / regulation of mitotic metaphase/anaphase transition / centrosome cycle / positive regulation of ubiquitin-protein transferase activity / 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 / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / 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 / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / 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 / cytoplasm / cytosol
Similarity search - Function
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 ...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 / 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
PL-2 / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLee, W.C. / Song, J.H. / Kim, H.Y.
CitationJournal: J.Med.Chem. / Year: 2015
Title: A new class of peptidomimetics targeting the polo-box domain of polo-like kinase 1.
Authors: Ahn, M. / Han, Y.H. / Park, J.E. / Kim, S. / Lee, W.C. / Lee, S.J. / Gunasekaran, P. / Cheong, C. / Shin, S.Y. / Kim, H.Y. / Ryu, E.K. / Murugan, R.N. / Kim, N.H. / Bang, J.K.
History
DepositionSep 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Structure summary
Revision 1.2Jan 21, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: PL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,62812
Polymers27,0082
Non-polymers62110
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint8 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.390, 61.270, 51.260
Angle α, β, γ (deg.)90.00, 103.27, 90.00
Int Tables number4
Space group name H-MP1211

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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: 26372.100 Da / Num. of mol.: 1 / Fragment: unp residues 372-599
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK, PLK1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53350, polo kinase
#2: Protein/peptide PL-2


Type: Polypeptide / Class: Inhibitor / Mass: 635.670 Da / Num. of mol.: 1 / Fragment: unp residues 1-5 / Source method: obtained synthetically / References: PL-2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4
Details: 0.2M sodium citrate pH 4.0, 500mM ammonium sulfate, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 30636 / % possible obs: 98.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.071 / Χ2: 1.048 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.662.70.36526710.499185.6
1.66-1.723.20.30130760.531199.8
1.72-1.83.30.23730950.594199.9
1.8-1.93.30.17931100.6991100
1.9-2.023.10.13430840.889199.9
2.02-2.173.40.10931071.1381100
2.17-2.393.50.09530931.2981100
2.39-2.743.30.07931121.344199.9
2.74-3.453.20.05831311.566199.9
3.45-503.20.04531571.68199

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2039 1464 4.7 %
Rwork0.189 --
obs-29555 94.2 %
Solvent computationBsol: 50.643 Å2
Displacement parametersBiso max: 52.35 Å2 / Biso mean: 19.5197 Å2 / Biso min: 10.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.249 Å20 Å2-1.695 Å2
2--4.871 Å20 Å2
3----3.622 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 40 163 2057
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.226
X-RAY DIFFRACTIONc_mcbond_it1.1041.5
X-RAY DIFFRACTIONc_scbond_it2.1282
X-RAY DIFFRACTIONc_mcangle_it1.7072
X-RAY DIFFRACTIONc_scangle_it3.1312.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.660.2441320.23161995212767.8
1.66-1.720.2641280.20612700282891
1.72-1.80.20681440.20042778292294.2
1.8-1.90.20661580.18422865302396
1.9-2.020.2091450.18092866301197.2
2.02-2.170.18131430.1722956309998.4
2.17-2.390.1941310.16842969310099.1
2.39-2.740.19411620.19162958312099.2
2.74-3.450.22521770.1992976315399.6
3.45-500.18851440.18973028317298.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2EDO.parEDO.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.paramCNS_TOPPAR:carbohydrate.top
X-RAY DIFFRACTION6capping.parcapping.top
X-RAY DIFFRACTION756A.par56A.top
X-RAY DIFFRACTION8TPO.parTPO.top

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