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- PDB-3fvh: Polo-like kinase 1 Polo box domain in complex with Ac-LHSpTA-NH2 ... -

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Basic information

Entry
Database: PDB / ID: 3fvh
TitlePolo-like kinase 1 Polo box domain in complex with Ac-LHSpTA-NH2 peptide
Components
  • Acetyl-Leu-His-Ser-phosphoThr-Ala-NH2 peptide
  • Serine/threonine-protein kinase PLK1
KeywordsCELL CYCLE / PEPTIDE BINDING PROTEIN / Polo like kinase 1 / Polo box domain / phosphopeptide binding domain / ATP-binding / Cell division / Kinase / Mitosis / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase / Transferase
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 / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / mitotic nuclear membrane disassembly / polo kinase / protein localization to nuclear envelope ...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 / sister chromatid cohesion / regulation of mitotic cell cycle phase transition / positive regulation of ubiquitin-protein transferase activity / 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 / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin A/B1/B2 associated events during G2/M transition / protein localization to chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / 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 / Condensation of Prophase Chromosomes / AURKA Activation by TPX2 / regulation of cytokinesis / mitotic spindle organization / RHO GTPases Activate Formins / establishment of protein localization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / protein destabilization / kinetochore / positive regulation of protein localization to nucleus / centriolar satellite / 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 / peptidyl-serine phosphorylation / microtubule cytoskeleton / midbody / microtubule binding / protein kinase activity / regulation of cell cycle / protein ubiquitination / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / negative regulation of apoptotic process / protein kinase binding / chromatin / 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 / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsLim, D.C. / Yaffe, M.B.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural and functional analyses of minimal phosphopeptides targeting the polo-box domain of polo-like kinase 1
Authors: Yun, S.M. / Moulaei, T. / Lim, D. / Bang, J.K. / Park, J.E. / Shenoy, S.R. / Liu, F. / Kang, Y.H. / Liao, C. / Soung, N.K. / Lee, S. / Yoon, D.Y. / Lim, Y. / Lee, D.H. / Otaka, A. / Appella, ...Authors: Yun, S.M. / Moulaei, T. / Lim, D. / Bang, J.K. / Park, J.E. / Shenoy, S.R. / Liu, F. / Kang, Y.H. / Liao, C. / Soung, N.K. / Lee, S. / Yoon, D.Y. / Lim, Y. / Lee, D.H. / Otaka, A. / Appella, E. / McMahon, J.B. / Nicklaus, M.C. / Burke, T.R. / Yaffe, M.B. / Wlodawer, A. / Lee, K.S.
History
DepositionJan 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 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
B: Acetyl-Leu-His-Ser-phosphoThr-Ala-NH2 peptide


Theoretical massNumber of molelcules
Total (without water)27,9182
Polymers27,9182
Non-polymers00
Water4,720262
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-6 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.310, 62.412, 46.607
Angle α, β, γ (deg.)90.00, 94.07, 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: 27285.158 Da / Num. of mol.: 1
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): Rosetta2 / References: UniProt: P53350, polo kinase
#2: Protein/peptide Acetyl-Leu-His-Ser-phosphoThr-Ala-NH2 peptide


Mass: 632.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 1.99 Å3/Da / Density % sol: 38.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 2000 MME, Tris pH 8.5, trimethyl-amine oxide, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 8, 2008 / Details: Osmic
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.58→25 Å / Num. all: 30083 / Num. obs: 28949 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.043 / Net I/σ(I): 17.4
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 8.6 / Num. unique all: 2834 / Rsym value: 0.172 / % possible all: 94.2

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Processing

Software
NameVersionClassification
StructureStudiodata collection
AMoREphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UMW

1umw


Resolution: 1.58→24.171 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1417 4.9 %random
Rwork0.1924 ---
obs0.1942 28941 96.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.962 Å2 / ksol: 0.395 e/Å3
Refinement stepCycle: LAST / Resolution: 1.58→24.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 0 262 2193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5804-1.63680.2731340.20092698X-RAY DIFFRACTION94
1.6368-1.70240.27661540.20192702X-RAY DIFFRACTION95
1.7024-1.77980.23951310.1992719X-RAY DIFFRACTION96
1.7798-1.87360.26891130.19982767X-RAY DIFFRACTION96
1.8736-1.99090.26291370.22362741X-RAY DIFFRACTION96
1.9909-2.14460.24421470.19252810X-RAY DIFFRACTION98
2.1446-2.36020.24011580.19382750X-RAY DIFFRACTION98
2.3602-2.70140.24461580.19792819X-RAY DIFFRACTION99
2.7014-3.40190.2541320.17922894X-RAY DIFFRACTION100
3.4019-24.17340.15961530.16892624X-RAY DIFFRACTION91

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