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- PDB-3bzi: Molecular and structural basis of polo-like kinase 1 substrate re... -

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Basic information

Entry
Database: PDB / ID: 3bzi
TitleMolecular and structural basis of polo-like kinase 1 substrate recognition: Implications in centrosomal localization
Components
  • 9 mer peptide from M-phase inducer phosphatase 3
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE / Kinase / cell cycle / localization / ATP-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


positive regulation of G2/MI transition of meiotic cell cycle / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / mitotic nuclear membrane disassembly / polo kinase ...positive regulation of G2/MI transition of meiotic cell cycle / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / mitotic nuclear membrane disassembly / polo kinase / protein localization to nuclear envelope / Phosphorylation of Emi1 / nuclear membrane disassembly / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / Phosphorylation of the APC/C / anaphase-promoting complex binding / outer kinetochore / positive regulation of ubiquitin protein ligase activity / double-strand break repair via alternative nonhomologous end joining / microtubule bundle formation / 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 / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / sister chromatid cohesion / regulation of mitotic cell cycle phase transition / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic nuclear division / WW domain binding / regulation of cyclin-dependent protein serine/threonine kinase activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / mitotic G2 DNA damage checkpoint signaling / regulation of anaphase-promoting complex-dependent catabolic process / establishment of mitotic spindle orientation / positive regulation of proteolysis / mitotic cytokinesis / mitotic sister chromatid segregation / phosphoprotein phosphatase activity / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Activation of ATR in response to replication stress / Cyclin A/B1/B2 associated events during G2/M transition / RHO GTPases activate PKNs / protein localization to chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of G2/M transition of mitotic cell cycle / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein tyrosine phosphatase activity / centriole / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / protein-tyrosine-phosphatase / Recruitment of mitotic centrosome proteins and complexes / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / regulation of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Condensation of Prophase Chromosomes / AURKA Activation by TPX2 / regulation of cytokinesis / mitotic spindle organization / RHO GTPases Activate Formins / establishment of protein localization / centriolar satellite / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / protein destabilization / kinetochore / mitochondrial intermembrane space / positive regulation of protein localization to nucleus / spindle / spindle pole / G2/M transition of mitotic cell cycle / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / mitotic cell cycle / microtubule cytoskeleton / peptidyl-serine phosphorylation / midbody / microtubule binding / spermatogenesis / cell population proliferation / protein kinase activity / regulation of cell cycle
Similarity search - Function
M-phase inducer phosphatase / M-phase inducer phosphatase / 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. ...M-phase inducer phosphatase / M-phase inducer phosphatase / 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 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like 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
FORMIC ACID / M-phase inducer phosphatase 3 / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGarcia-Alvarez, B. / de Carcer, G. / Ibanez, S. / Bragado-Nilsson, E. / Montoya, G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Molecular and structural basis of polo-like kinase 1 substrate recognition: Implications in centrosomal localization.
Authors: Garcia-Alvarez, B. / de Carcer, G. / Ibanez, S. / Bragado-Nilsson, E. / Montoya, G.
History
DepositionJan 18, 2008Deposition site: RCSB / Processing site: PDBJ
SupersessionFeb 5, 2008ID: 2OJS
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
E: 9 mer peptide from M-phase inducer phosphatase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5453
Polymers28,4992
Non-polymers461
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.726, 67.481, 87.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 27502.334 Da / Num. of mol.: 1 / Fragment: Polo Box Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1 / Plasmid: pGEX-6-1P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Rosetta / References: UniProt: P53350, polo kinase
#2: Protein/peptide 9 mer peptide from M-phase inducer phosphatase 3 / 9 mer peptide from Dual specificity phosphatase Cdc25C


Mass: 997.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P30307
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
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: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 100mM HEPES pH 7.5, 2M ammonium formate, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→36.84 Å / Num. all: 13378 / Num. obs: 12144 / % possible obs: 90.77 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1owl

1owl


Resolution: 2.1→36.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.194 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24579 627 4.9 %RANDOM
Rwork0.17434 ---
obs0.17785 12144 90.77 %-
all-13378 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.739 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 0 175 2040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221905
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.9772576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6255228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11223.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93915339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9751516
X-RAY DIFFRACTIONr_chiral_restr0.1330.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021423
X-RAY DIFFRACTIONr_nbd_refined0.2250.2843
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21309
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2140
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.216
X-RAY DIFFRACTIONr_mcbond_it1.2091.51181
X-RAY DIFFRACTIONr_mcangle_it2.04621850
X-RAY DIFFRACTIONr_scbond_it3.1953829
X-RAY DIFFRACTIONr_scangle_it4.7374.5726
LS refinement shellResolution: 2.097→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 40 -
Rwork0.203 844 -
obs--87.09 %

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