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- PDB-1q4o: The structure of the polo box domain of human Plk1 -

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Basic information

Entry
Database: PDB / ID: 1q4o
TitleThe structure of the polo box domain of human Plk1
ComponentsSerine/threonine-protein kinase PLK
KeywordsTRANSFERASE / Serine/threonine-protein kinase / ATP-binding / Nuclear protein
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / regulation of protein binding / Activation of NIMA Kinases NEK9, NEK6, NEK7 / nuclear membrane disassembly / homologous chromosome segregation / polo kinase ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / regulation of protein binding / Activation of NIMA Kinases NEK9, NEK6, NEK7 / nuclear membrane disassembly / homologous chromosome segregation / polo kinase / mitotic nuclear membrane disassembly / Phosphorylation of Emi1 / protein localization to nuclear envelope / metaphase/anaphase transition of mitotic cell cycle / double-strand break repair via alternative nonhomologous end joining / synaptonemal complex / female meiosis chromosome segregation / anaphase-promoting complex binding / Phosphorylation of the APC/C / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of mitotic spindle assembly / positive regulation of ubiquitin protein ligase activity / microtubule bundle formation / mitotic chromosome condensation / Polo-like kinase mediated events / 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 / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / establishment of mitotic spindle orientation / positive regulation of proteolysis / mitotic sister chromatid segregation / mitotic cytokinesis / centriolar satellite / negative regulation of double-strand break repair via homologous recombination / spindle midzone / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / 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 / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / centriole / AURKA Activation by TPX2 / mitotic spindle organization / Condensation of Prophase Chromosomes / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / RHO GTPases Activate Formins / protein destabilization / establishment of protein localization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / kinetochore / spindle pole / positive regulation of protein localization to nucleus / spindle / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / G2/M transition of mitotic cell cycle / 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 / peptidyl-serine phosphorylation / microtubule binding / 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 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
Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsCheng, K.Y. / Lowe, E.D. / Sinclair, J. / Nigg, E.A. / Johnson, L.N.
CitationJournal: Embo J. / Year: 2003
Title: The crystal structure of the human polo-like kinase-1 polo box domain and its phospho-peptide complex.
Authors: Cheng, K.Y. / Lowe, E.D. / Sinclair, J. / Nigg, E.A. / Johnson, L.N.
History
DepositionAug 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK
B: Serine/threonine-protein kinase PLK


Theoretical massNumber of molelcules
Total (without water)54,5442
Polymers54,5442
Non-polymers00
Water4,089227
1
A: Serine/threonine-protein kinase PLK


Theoretical massNumber of molelcules
Total (without water)27,2721
Polymers27,2721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase PLK


Theoretical massNumber of molelcules
Total (without water)27,2721
Polymers27,2721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.741, 42.021, 80.727
Angle α, β, γ (deg.)103.16, 93.88, 91.32
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 27272.113 Da / Num. of mol.: 2 / Fragment: Polo box domain of Plk1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK OR PLK1 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) pLysS
References: UniProt: P53350, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 4000, sodium citrate and ammonium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
25-10 %(v/v)PEG40001reservoir
30.1 Msodium citrate1reservoirpH6.0
40.1 Mammonium acetate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONELETTRA 5.2R10.998
SYNCHROTRONESRF ID2920.9792
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDJun 6, 2003mirrors
ADSC QUANTUM 42CCDJul 6, 2003mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si monchromator and toroidal focusing mirrorSINGLE WAVELENGTHMx-ray1
2Si monchromator and cylindrical grazing incidence mirrorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9981
20.97921
ReflectionResolution: 2.2→20 Å / Num. all: 21172 / Num. obs: 20156 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 31.2 Å2 / Rsym value: 0.05 / Net I/σ(I): 8.4
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.146 / % possible all: 92
Reflection
*PLUS
Num. measured all: 103961 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.146

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
REFMAC5.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD
Starting model: Model derived from a SOLVE phased map from data of a Se-Met derivative

Resolution: 2.2→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1041 -Random
Rwork0.198 ---
all0.203 20156 --
obs0.198 19093 95.2 %-
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20.22 Å20.45 Å2
2---0.88 Å2-1.86 Å2
3---1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 0 227 3622
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.017
X-RAY DIFFRACTIONr_bond_other_d0.002
X-RAY DIFFRACTIONr_angle_refined_deg1.72
X-RAY DIFFRACTIONr_angle_other_deg0.9
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62
LS refinement shellResolution: 2.2→2.257 Å
RfactorNum. reflection% reflection
Rfree0.352 78 -
Rwork0.227 --
obs-1266 92 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.017
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.72

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