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- PDB-3q1i: Polo-like kinase I Polo-box domain in complex with FMPPPMSpSM pho... -

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Basic information

Entry
Database: PDB / ID: 3q1i
TitlePolo-like kinase I Polo-box domain in complex with FMPPPMSpSM phosphopeptide from TCERG1
Components
  • Serine/threonine-protein kinase PLK1
  • peptide from Transcription elongation regulator 1
KeywordsTRANSFERASE / KINASE / PEPTIDE BINDING PROTEIN / Plk1
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 / transcription elongation factor activity / mitotic chromosome condensation / Polo-like kinase mediated events / regulation of mitotic spindle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / centrosome cycle / RNA polymerase binding / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / ubiquitin-like protein conjugating enzyme binding / 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 / negative regulation of transcription elongation by RNA polymerase II / 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 / mRNA Splicing - Major Pathway / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / RNA splicing / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / AURKA Activation by TPX2 / regulation of cytokinesis / mitotic spindle organization / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / 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 / mRNA processing / spindle pole / transcription corepressor activity / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / protein kinase activity / regulation of cell cycle / nuclear speck / protein ubiquitination / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / negative regulation of apoptotic process / protein kinase binding
Similarity search - Function
Transcription elongation regulator 1-like / TCERG1 WW domain / POLO box domain / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / Polo-like kinase 1, catalytic domain / Second polo-box domain ...Transcription elongation regulator 1-like / TCERG1 WW domain / POLO box domain / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / 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 / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW 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
DI(HYDROXYETHYL)ETHER / Transcription elongation regulator 1 / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSledz, P. / Hyvonen, M. / Abell, C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: From crystal packing to molecular recognition: prediction and discovery of a binding site on the surface of polo-like kinase 1
Authors: Sledz, P. / Stubbs, C.J. / Lang, S. / Yang, Y.Q. / McKenzie, G.J. / Venkitaraman, A.R. / Hyvonen, M. / Abell, C.
History
DepositionDec 17, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: 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_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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
E: peptide from Transcription elongation regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3485
Polymers27,8842
Non-polymers4653
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-7 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.500, 51.500, 57.600
Angle α, β, γ (deg.)90.00, 101.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AE

#1: Protein Serine/threonine-protein kinase PLK1 / Polo-like kinase 1 / PLK-1 / Serine/threonine-protein kinase 13 / STPK13


Mass: 26755.518 Da / Num. of mol.: 1 / Fragment: Polo-box domain, residues 371-594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Production host: Escherichia coli (E. coli) / References: UniProt: P53350, polo kinase
#2: Protein/peptide peptide from Transcription elongation regulator 1 / peptide from TCERG1


Mass: 1128.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic phosphopeptide / References: UniProt: O14776

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Non-polymers , 4 types, 195 molecules

#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.85 Å3/Da / Density % sol: 33.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9184 Å
DetectorDate: Nov 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→56.54 Å / Num. all: 40284 / Num. obs: 38959 / % possible obs: 97 %

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UMW chain A

1umw


Resolution: 1.4→56.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.994 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22156 1939 5 %RANDOM
Rwork0.19723 ---
obs0.19844 37019 96.75 %-
all-40284 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.809 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.37 Å2
2--0.28 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.4→56.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 31 192 2002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0211887
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9681.9822559
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3125238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64923.04982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72715.047320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7811514
X-RAY DIFFRACTIONr_chiral_restr0.0670.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211397
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3691.51142
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74421849
X-RAY DIFFRACTIONr_scbond_it1.1223745
X-RAY DIFFRACTIONr_scangle_it1.8464.5701
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 140 -
Rwork0.232 2697 -
obs--95.23 %
Refinement TLS params.Method: refined / Origin x: 8.095 Å / Origin y: -0.323 Å / Origin z: 14.42 Å
111213212223313233
T0.0103 Å20.0077 Å2-0.0087 Å2-0.0064 Å2-0.0063 Å2--0.0121 Å2
L0.6416 °20.3048 °2-0.6414 °2-0.3004 °2-0.3046 °2--1.5407 °2
S0.0044 Å °-0.0039 Å °-0.0232 Å °-0.0011 Å °-0.0116 Å °-0.0066 Å °0.063 Å °0.0578 Å °0.0071 Å °

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