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- PDB-5x3s: Crystal structure of mouse Plk1-PBD in complex with phosphopeptid... -

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Basic information

Entry
Database: PDB / ID: 5x3s
TitleCrystal structure of mouse Plk1-PBD in complex with phosphopeptide from HEF1 (799-809)
Components
  • Peptide from Enhancer of filamentation 1
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE/PEPTIDE / Polo like kinase 1 / plk1 / Polo-box domain / HEF1 / TRANSFERASE / TRANSFERASE-PEPTIDE complex
Function / homology
Function and homology information


positive regulation of lymphocyte chemotaxis / positive regulation of immunological synapse formation / Polo-like kinase mediated events / Phosphorylation of the APC/C / Phosphorylation of Emi1 / Mitotic Metaphase/Anaphase Transition / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Golgi Cisternae Pericentriolar Stack Reorganization / Mitotic Telophase/Cytokinesis / Cyclin A/B1/B2 associated events during G2/M transition ...positive regulation of lymphocyte chemotaxis / positive regulation of immunological synapse formation / Polo-like kinase mediated events / Phosphorylation of the APC/C / Phosphorylation of Emi1 / Mitotic Metaphase/Anaphase Transition / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Golgi Cisternae Pericentriolar Stack Reorganization / Mitotic Telophase/Cytokinesis / Cyclin A/B1/B2 associated events during G2/M transition / polar body extrusion after meiotic divisions / Condensation of Prophase Chromosomes / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / lymphocyte migration into lymphoid organs / protein localization to organelle / regulation of protein localization to cell cortex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / synaptonemal complex disassembly / The role of GTSE1 in G2/M progression after G2 checkpoint / homologous chromosome segregation / nuclear membrane disassembly / RHO GTPases Activate Formins / polo kinase / Separation of Sister Chromatids / protein localization to nuclear envelope / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / synaptonemal complex / Regulation of PLK1 Activity at G2/M Transition / female meiosis chromosome segregation / anaphase-promoting complex binding / outer kinetochore / condensed chromosome, centromeric region / positive regulation of ubiquitin protein ligase activity / cilium disassembly / regulation of mitotic spindle assembly / microtubule bundle formation / positive regulation of osteoclast differentiation / positive regulation of ubiquitin-protein transferase activity / centrosome cycle / positive regulation of protein localization / mitotic spindle assembly checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / mitotic spindle pole / mitotic G2 DNA damage checkpoint signaling / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / actin filament bundle assembly / chromosome, centromeric region / immunological synapse / positive regulation of protein tyrosine kinase activity / centriolar satellite / mitotic cytokinesis / positive regulation of dendritic spine maintenance / spindle midzone / negative regulation of double-strand break repair via homologous recombination / positive regulation of substrate adhesion-dependent cell spreading / protein localization to chromatin / cytoskeleton organization / cell surface receptor protein tyrosine kinase signaling pathway / centriole / negative regulation of cell migration / protein tyrosine kinase binding / ciliary basal body / mitotic spindle organization / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein destabilization / establishment of protein localization / spindle microtubule / mitotic spindle / kinetochore / spindle pole / spindle / G2/M transition of mitotic cell cycle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cell migration / lamellipodium / mitotic cell cycle / cell cortex / midbody / microtubule binding / basolateral plasma membrane / learning or memory / cell adhesion / protein kinase activity / protein ubiquitination / positive regulation of cell migration / cell cycle / cell division / protein phosphorylation
Similarity search - Function
Enhancer of filamentation 1, SH3 domain / Serine rich protein interaction domain / CAS family, C-terminal / CAS family / CAS, serine rich four helix bundle domain superfamily / Serine rich protein interaction domain / Crk-Associated Substrate C-terminal domain / POLO box domain / Polo-like kinase 1, catalytic domain / Second polo-box domain ...Enhancer of filamentation 1, SH3 domain / Serine rich protein interaction domain / CAS family, C-terminal / CAS family / CAS, serine rich four helix bundle domain superfamily / Serine rich protein interaction domain / Crk-Associated Substrate C-terminal domain / 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 / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 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 / Enhancer of filamentation 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.899 Å
AuthorsKim, J.H. / Shin, S.C. / Kim, E.E.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Phosphorylation of human enhancer filamentation 1 (HEF1) stimulates interaction with Polo-like kinase 1 leading to HEF1 localization to focal adhesions.
Authors: Lee, K.H. / Hwang, J.A. / Kim, S.O. / Kim, J.H. / Shin, S.C. / Kim, E.E. / Lee, K.S. / Rhee, K. / Jeon, B.H. / Bang, J.K. / Cha-Molstad, H. / Soung, N.K. / Jang, J.H. / Ko, S.K. / Lee, H.G. ...Authors: Lee, K.H. / Hwang, J.A. / Kim, S.O. / Kim, J.H. / Shin, S.C. / Kim, E.E. / Lee, K.S. / Rhee, K. / Jeon, B.H. / Bang, J.K. / Cha-Molstad, H. / Soung, N.K. / Jang, J.H. / Ko, S.K. / Lee, H.G. / Ahn, J.S. / Kwon, Y.T. / Kim, B.Y.
History
DepositionFeb 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Serine/threonine-protein kinase PLK1
A: Serine/threonine-protein kinase PLK1
C: Peptide from Enhancer of filamentation 1
D: Peptide from Enhancer of filamentation 1


Theoretical massNumber of molelcules
Total (without water)54,4784
Polymers54,4784
Non-polymers00
Water1267
1
B: Serine/threonine-protein kinase PLK1
D: Peptide from Enhancer of filamentation 1


Theoretical massNumber of molelcules
Total (without water)27,2392
Polymers27,2392
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-8 kcal/mol
Surface area11590 Å2
MethodPISA
2
A: Serine/threonine-protein kinase PLK1
C: Peptide from Enhancer of filamentation 1


Theoretical massNumber of molelcules
Total (without water)27,2392
Polymers27,2392
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-10 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.564, 59.402, 72.748
Angle α, β, γ (deg.)90.000, 99.470, 90.000
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: 25898.502 Da / Num. of mol.: 2 / Fragment: UNP residues 371-594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plk1, Plk / Production host: Escherichia coli (E. coli) / References: UniProt: Q07832, polo kinase
#2: Protein/peptide Peptide from Enhancer of filamentation 1 / hEF1 / CRK-associated substrate-related protein / CasL / Cas scaffolding protein family member 2 / ...hEF1 / CRK-associated substrate-related protein / CasL / Cas scaffolding protein family member 2 / Neural precursor cell expressed developmentally down-regulated protein 9 / NEDD-9 / Renal carcinoma antigen NY-REN-12 / p105


Mass: 1340.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14511
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 15% PEG 6000, 0.1M sodium citrate / PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 9198 / % possible obs: 84.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.097 / Rrim(I) all: 0.182 / Χ2: 1.783 / Net I/σ(I): 5.6 / Num. measured all: 23782
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-31.70.2720.6170.2250.3550.43467.3
3-3.121.80.2420.830.1960.3130.55974
3.12-3.2720.2380.8520.1820.3020.67978.5
3.27-3.442.20.2190.8710.1640.2760.76581.4
3.44-3.652.30.2040.9160.140.2491.31683.9
3.65-3.942.70.1830.9360.1210.2211.25689.1
3.94-4.332.90.1590.9680.10.191.82992.2
4.33-4.963.10.140.9650.0880.1672.06692.9
4.96-6.243.10.1340.9710.0810.1581.76292.3
6.24-503.50.1140.9820.0660.1333.44991.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HIK

3hik


Resolution: 2.899→33.93 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 22.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 450 4.9 %
Rwork0.2025 8739 -
obs0.2045 9189 84.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.68 Å2 / Biso mean: 38.6935 Å2 / Biso min: 14.67 Å2
Refinement stepCycle: final / Resolution: 2.899→33.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3746 0 0 7 3753
Biso mean---30.63 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043828
X-RAY DIFFRACTIONf_angle_d0.6625189
X-RAY DIFFRACTIONf_chiral_restr0.044580
X-RAY DIFFRACTIONf_plane_restr0.003657
X-RAY DIFFRACTIONf_dihedral_angle_d15.4762301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8994-3.31860.30411360.24122518265473
3.3186-4.17990.26161460.20232985313187
4.1799-33.93240.20941680.1883236340492

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