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- PDB-1q4k: The polo-box domain of Plk1 in complex with a phospho-peptide -

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Basic information

Entry
Database: PDB / ID: 1q4k
TitleThe polo-box domain of Plk1 in complex with a phospho-peptide
Components
  • Phospho-peptide sequence Met.Gln.Ser.pThr.Pro.Leu
  • Serine/threonine-protein kinase PLK
KeywordsTRANSFERASE / Six-stranded anti-parallel beta sheet with one alpha helix
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 / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / nuclear membrane disassembly / polo kinase / mitotic nuclear membrane disassembly ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / nuclear membrane disassembly / polo kinase / mitotic nuclear membrane disassembly / protein localization to nuclear envelope / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / regulation of protein binding / anaphase-promoting complex binding / Phosphorylation of the APC/C / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / regulation of mitotic spindle assembly / microtubule bundle formation / Polo-like kinase mediated events / mitotic chromosome condensation / Golgi Cisternae Pericentriolar Stack Reorganization / sister chromatid cohesion / regulation of mitotic metaphase/anaphase transition / centrosome cycle / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / positive regulation of proteolysis / centriolar satellite / mitotic cytokinesis / spindle midzone / negative regulation of double-strand break repair via homologous recombination / 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 / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / centriole / AURKA Activation by TPX2 / Condensation of Prophase Chromosomes / mitotic spindle organization / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / 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 pole / positive regulation of protein localization to nucleus / spindle / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / The role of GTSE1 in G2/M progression after G2 checkpoint / 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 / microtubule binding / peptidyl-serine phosphorylation / 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 / cytoplasm / 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
Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCheng, K. / 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 1.3Apr 3, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE No sequence database reference found for phospho-peptide (entity 2, chains D,E,F)at the ...SEQUENCE No sequence database reference found for phospho-peptide (entity 2, chains D,E,F)at the time of processing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Serine/threonine-protein kinase PLK
A: Serine/threonine-protein kinase PLK
C: Serine/threonine-protein kinase PLK
D: Phospho-peptide sequence Met.Gln.Ser.pThr.Pro.Leu
E: Phospho-peptide sequence Met.Gln.Ser.pThr.Pro.Leu
F: Phospho-peptide sequence Met.Gln.Ser.pThr.Pro.Leu


Theoretical massNumber of molelcules
Total (without water)91,8536
Polymers91,8536
Non-polymers00
Water3,441191
1
B: Serine/threonine-protein kinase PLK
E: Phospho-peptide sequence Met.Gln.Ser.pThr.Pro.Leu


Theoretical massNumber of molelcules
Total (without water)30,6182
Polymers30,6182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-9 kcal/mol
Surface area11720 Å2
MethodPISA
2
A: Serine/threonine-protein kinase PLK
D: Phospho-peptide sequence Met.Gln.Ser.pThr.Pro.Leu


Theoretical massNumber of molelcules
Total (without water)30,6182
Polymers30,6182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-9 kcal/mol
Surface area11570 Å2
MethodPISA
3
C: Serine/threonine-protein kinase PLK
F: Phospho-peptide sequence Met.Gln.Ser.pThr.Pro.Leu


Theoretical massNumber of molelcules
Total (without water)30,6182
Polymers30,6182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-8 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.071, 56.888, 85.050
Angle α, β, γ (deg.)91.45, 103.21, 118.50
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: 29862.035 Da / Num. of mol.: 3 / Fragment: Polo box domain of human Plk1 / Mutation: residues 345-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 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: Protein/peptide Phospho-peptide sequence Met.Gln.Ser.pThr.Pro.Leu


Mass: 755.774 Da / Num. of mol.: 3 / Fragment: Phospho-peptide / Mutation: sequence Met.Gln.Ser.pThr.Pro.Leu / Source method: obtained synthetically / Details: Chemical synthesis
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21-10 %PEG200001reservoir
30.1 MMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 6, 2003 / Details: mirrors
RadiationMonochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→29.36 Å / Num. all: 38616 / Num. obs: 37228 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 49.7 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.096 / Net I/σ(I): 2.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5668 / Rsym value: 0.258 / % possible all: 96.6
Reflection
*PLUS
Lowest resolution: 24.7 Å / Num. obs: 35628 / Num. measured all: 71256 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.258

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unliganded polo box domain

Resolution: 2.3→29.36 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.861 / SU B: 7.791 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.373 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31166 1943 5 %RANDOM
Rwork0.24502 ---
all0.248 36665 --
obs0.24832 36665 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.646 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å2-0.01 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5516 0 0 191 5707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215628
X-RAY DIFFRACTIONr_bond_other_d0.0020.025100
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.977608
X-RAY DIFFRACTIONr_angle_other_deg1.269311854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2135671
X-RAY DIFFRACTIONr_chiral_restr0.090.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026138
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021185
X-RAY DIFFRACTIONr_nbd_refined0.2010.21264
X-RAY DIFFRACTIONr_nbd_other0.2290.26263
X-RAY DIFFRACTIONr_nbtor_other0.0940.23546
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2199
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3370.212
X-RAY DIFFRACTIONr_mcbond_it0.7071.53377
X-RAY DIFFRACTIONr_mcangle_it1.34125450
X-RAY DIFFRACTIONr_scbond_it1.77832251
X-RAY DIFFRACTIONr_scangle_it3.0484.52158
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 153
Rwork0.26 2705
Refinement
*PLUS
Lowest resolution: 24.7 Å / Rfactor Rfree: 0.313 / Rfactor Rwork: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.67

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