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- PDB-5j19: phospho-Pon binding-induced Plk1 dimerization -

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Basic information

Entry
Database: PDB / ID: 5j19
Titlephospho-Pon binding-induced Plk1 dimerization
Components
  • Phosphorylated peptide from Partner of Numb
  • Serine/threonine-protein kinase PLK1
KeywordsCELL CYCLE / Polo-box domain
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 / asymmetric neuroblast division / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / homologous chromosome segregation / protein localization to nuclear envelope ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / asymmetric neuroblast division / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / homologous chromosome segregation / protein localization to nuclear envelope / polo kinase / nuclear membrane disassembly / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / basal part of cell / Phosphorylation of the APC/C / anaphase-promoting complex binding / regulation of protein binding / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / double-strand break repair via alternative nonhomologous end joining / positive regulation of ubiquitin protein ligase activity / regulation of mitotic spindle assembly / microtubule bundle formation / embryonic heart tube development / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / mitotic chromosome condensation / regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin-protein transferase activity / centrosome cycle / sister chromatid cohesion / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / mitotic sister chromatid segregation / positive regulation of proteolysis / establishment of mitotic spindle orientation / mitotic cytokinesis / centriolar satellite / spindle midzone / 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 / regulation of mitotic cell cycle / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / mitotic spindle organization / Condensation of Prophase Chromosomes / 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 / spindle pole / positive regulation of protein localization to nucleus / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / cell cortex / midbody / microtubule binding / peptidyl-serine phosphorylation / protein ubiquitination / regulation of cell cycle / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / chromatin / negative regulation of apoptotic process / protein kinase binding / magnesium ion binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / nucleus / 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
Partner of Numb / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
Model detailsPhospho-Pon binding mediated fine tuning of Plk1 activity
AuthorsZhu, K. / Shan, Z. / Zhang, L. / Wen, W.
CitationJournal: Structure / Year: 2016
Title: Phospho-Pon Binding-Mediated Fine-Tuning of Plk1 Activity
Authors: Zhu, K. / Shan, Z. / Zhang, L. / Wen, W.
History
DepositionMar 29, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: Phosphorylated peptide from Partner of Numb
D: Phosphorylated peptide from Partner of Numb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5357
Polymers57,2594
Non-polymers2763
Water1,910106
1
A: Serine/threonine-protein kinase PLK1
D: Phosphorylated peptide from Partner of Numb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7223
Polymers28,6292
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-8 kcal/mol
Surface area11070 Å2
MethodPISA
2
B: Serine/threonine-protein kinase PLK1
C: Phosphorylated peptide from Partner of Numb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8144
Polymers28,6292
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-9 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.880, 91.997, 159.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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: 26929.672 Da / Num. of mol.: 2 / Fragment: Polo-box domain, UNP residues 367-594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P53350, polo kinase
#2: Protein/peptide Phosphorylated peptide from Partner of Numb / PON


Mass: 1699.773 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: O96561
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.81 Å3/Da / Density % sol: 56.26 % / Mosaicity: 0.811 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 5.5 / Details: PEG 3350, NaCOOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.953 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 42369 / % possible obs: 98.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 33.48 Å2 / Rmerge(I) obs: 0.082 / Χ2: 2.512 / Net I/av σ(I): 32.875 / Net I/σ(I): 12.7 / Num. measured all: 233958
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.035.90.6221451.73100
2.03-2.075.80.53921161.859100
2.07-2.115.80.48121341.997100
2.11-2.155.80.37821231.94100
2.15-2.25.80.32321042.055100
2.2-2.255.80.29521492.203100
2.25-2.315.80.27121152.351100
2.31-2.375.80.23321112.333100
2.37-2.445.80.19321342.485100
2.44-2.525.70.17521522.562100
2.52-2.615.70.14921212.632100
2.61-2.715.70.12621292.999.9
2.71-2.845.60.10521433.012100
2.84-2.995.60.09121553.337100
2.99-3.175.40.0821453.009100
3.17-3.425.30.0721343.0999.6
3.42-3.7650.06321093.19197.6
3.76-4.314.80.05420432.85793.2
4.31-5.434.50.04519902.34190.7
5.43-5050.0421172.73191.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UMW

1umw


Resolution: 2→39.828 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.46
RfactorNum. reflection% reflection
Rfree0.2356 2099 5.02 %
Rwork0.213 --
obs0.2142 41823 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.09 Å2 / Biso mean: 33.93 Å2 / Biso min: 16.37 Å2
Refinement stepCycle: final / Resolution: 2→39.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3573 0 18 106 3697
Biso mean--44.35 31.08 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093674
X-RAY DIFFRACTIONf_angle_d1.1614990
X-RAY DIFFRACTIONf_chiral_restr0.077567
X-RAY DIFFRACTIONf_plane_restr0.005627
X-RAY DIFFRACTIONf_dihedral_angle_d13.4311286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.04650.31221350.270826672802100
2.0465-2.09770.28551420.258126432785100
2.0977-2.15440.28771500.236826722822100
2.1544-2.21780.27561320.229526512783100
2.2178-2.28940.28831280.218226492777100
2.2894-2.37120.2871430.22326662809100
2.3712-2.46610.2491420.217526532795100
2.4661-2.57840.26571480.237626852833100
2.5784-2.71430.26071420.234726732815100
2.7143-2.88430.28721570.235226512808100
2.8843-3.10690.26871480.223826812829100
3.1069-3.41940.22811350.225526882823100
3.4194-3.91380.23781320.20212664279698
3.9138-4.92960.17951180.16782433255189
4.9296-39.83620.18761470.20512648279593
Refinement TLS params.Method: refined / Origin x: -31.3262 Å / Origin y: -11.5186 Å / Origin z: -20.0538 Å
111213212223313233
T0.221 Å20.0053 Å20.0176 Å2-0.2181 Å20.013 Å2--0.1539 Å2
L1.4907 °20.6895 °20.5265 °2-0.6798 °20.2037 °2--0.8008 °2
S0.0092 Å °-0.0104 Å °-0.0473 Å °-0.0129 Å °-0.0046 Å °-0.0053 Å °0.0149 Å °0.0315 Å °-0.0129 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA371 - 593
2X-RAY DIFFRACTION1allB365 - 594
3X-RAY DIFFRACTION1allC57 - 65
4X-RAY DIFFRACTION1allD58 - 65
5X-RAY DIFFRACTION1allE1 - 29
6X-RAY DIFFRACTION1allE30 - 37
7X-RAY DIFFRACTION1allE38 - 54
8X-RAY DIFFRACTION1allE55 - 75
9X-RAY DIFFRACTION1allE76 - 88
10X-RAY DIFFRACTION1allE89 - 99
11X-RAY DIFFRACTION1allE100 - 106
12X-RAY DIFFRACTION1allF1 - 2
13X-RAY DIFFRACTION1allF3

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