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- PDB-5dms: Mouse Polo-box domain and Emi2 (169-177) -

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Basic information

Entry
Database: PDB / ID: 5dms
TitleMouse Polo-box domain and Emi2 (169-177)
Components
  • F-box only protein 43
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE/METAL BINDING PROTEIN / PLK1 / Emi2 / Protein Kinase / meiosis / TRANSFERASE-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


Polo-like kinase mediated events / Phosphorylation of the APC/C / Phosphorylation of Emi1 / Mitotic Metaphase/Anaphase Transition / Activation of NIMA Kinases NEK9, NEK6, NEK7 / synaptonemal complex disassembly / Golgi Cisternae Pericentriolar Stack Reorganization / regulation of meiotic nuclear division / negative regulation of cell cycle process / female meiosis chromosome segregation ...Polo-like kinase mediated events / Phosphorylation of the APC/C / Phosphorylation of Emi1 / Mitotic Metaphase/Anaphase Transition / Activation of NIMA Kinases NEK9, NEK6, NEK7 / synaptonemal complex disassembly / Golgi Cisternae Pericentriolar Stack Reorganization / regulation of meiotic nuclear division / negative regulation of cell cycle process / female meiosis chromosome segregation / Mitotic Telophase/Cytokinesis / Cyclin A/B1/B2 associated events during G2/M transition / negative regulation of meiotic nuclear division / Condensation of Prophase Chromosomes / polar body extrusion after meiotic divisions / homologous chromosome segregation / centrosome separation / protein localization to nuclear envelope / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / nuclear membrane disassembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / regulation of protein localization to cell cortex / positive regulation of mitotic nuclear envelope disassembly / protein localization to centrosome / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / The role of GTSE1 in G2/M progression after G2 checkpoint / polo kinase / RHO GTPases Activate Formins / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Separation of Sister Chromatids / Anchoring of the basal body to the plasma membrane / Recruitment of NuMA to mitotic centrosomes / AURKA Activation by TPX2 / anaphase-promoting complex binding / synaptonemal complex / astral microtubule organization / Regulation of PLK1 Activity at G2/M Transition / mitotic cleavage furrow formation / outer kinetochore / condensed chromosome, centromeric region / microtubule bundle formation / double-strand break repair via alternative nonhomologous end joining / regulation of mitotic spindle assembly / protein localization to site of double-strand break / positive regulation of mitotic metaphase/anaphase transition / centrosome cycle / positive regulation of ubiquitin-dependent protein catabolic process / regulation of mitotic nuclear division / regulation of mitotic metaphase/anaphase transition / centriolar satellite / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / spindle midzone / establishment of mitotic spindle orientation / mitotic G2 DNA damage checkpoint signaling / positive regulation of proteolysis / mitotic sister chromatid segregation / mitotic cytokinesis / chromosome, centromeric region / negative regulation of double-strand break repair via homologous recombination / protein localization to chromatin / centriole / mitotic spindle organization / regulation of mitotic cell cycle / regulation of cytokinesis / spindle microtubule / establishment of protein localization / G2/M transition of mitotic cell cycle / negative regulation of protein catabolic process / protein destabilization / meiotic cell cycle / peptidyl-serine phosphorylation / double-strand break repair via homologous recombination / spindle / kinetochore / spindle pole / microtubule cytoskeleton / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / microtubule binding / protein kinase activity / protein phosphorylation / protein ubiquitination / 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 / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function
FBXO43 helical domain / Zinc finger ZBR-type domain / : / Zinc finger ZBR-type profile. / 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 ...FBXO43 helical domain / Zinc finger ZBR-type domain / : / Zinc finger ZBR-type profile. / 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 / IBR domain / In Between Ring fingers / Arylsulfatase, C-terminal domain / POLO box domain / POLO box domain profile. / 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 / F-box only protein 43
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.89999 Å
AuthorsNamgoong, S.
CitationJournal: Sci Rep / Year: 2015
Title: Structural basis for recognition of Emi2 by Polo-like kinase 1 and development of peptidomimetics blocking oocyte maturation and fertilization.
Authors: Jia, J.L. / Han, Y.H. / Kim, H.C. / Ahn, M. / Kwon, J.W. / Luo, Y. / Gunasekaran, P. / Lee, S.J. / Lee, K.S. / Bang, J.K. / Kim, N.H. / Namgoong, S.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
B: F-box only protein 43
C: Serine/threonine-protein kinase PLK1
D: F-box only protein 43


Theoretical massNumber of molelcules
Total (without water)56,7464
Polymers56,7464
Non-polymers00
Water4,252236
1
A: Serine/threonine-protein kinase PLK1
B: F-box only protein 43


Theoretical massNumber of molelcules
Total (without water)28,3732
Polymers28,3732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-7 kcal/mol
Surface area11200 Å2
MethodPISA
2
C: Serine/threonine-protein kinase PLK1
D: F-box only protein 43


Theoretical massNumber of molelcules
Total (without water)28,3732
Polymers28,3732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-8 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.820, 70.450, 59.150
Angle α, β, γ (deg.)90.00, 90.13, 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: 27242.980 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 367-603
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 F-box only protein 43 / Endogenous meiotic inhibitor 2


Mass: 1130.146 Da / Num. of mol.: 2 / Fragment: Emi2 Peptide (UNP RESIDUES 169-177) / Source method: obtained synthetically / Details: FSQHKTS(TPO)I / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8CDI2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 15% polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 20, 2013
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89999→35.4 Å / Num. obs: 36843 / % possible obs: 98.4 % / Redundancy: 7.4 % / Net I/σ(I): 21.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 6 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1688refinement
HKL-2000data reduction
RefinementResolution: 1.89999→35.392 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 1974 5.36 %Random selection
Rwork0.1951 ---
obs0.1976 36843 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89999→35.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3719 0 0 236 3955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073801
X-RAY DIFFRACTIONf_angle_d1.0625153
X-RAY DIFFRACTIONf_dihedral_angle_d14.5771408
X-RAY DIFFRACTIONf_chiral_restr0.043583
X-RAY DIFFRACTIONf_plane_restr0.004649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.94650.40831330.31292429X-RAY DIFFRACTION100
1.9465-1.99910.321430.27082507X-RAY DIFFRACTION100
1.9991-2.05790.28661540.22642455X-RAY DIFFRACTION100
2.0579-2.12430.28471400.22052478X-RAY DIFFRACTION100
2.1243-2.20020.28921420.20412494X-RAY DIFFRACTION100
2.2002-2.28830.26851430.19452482X-RAY DIFFRACTION100
2.2883-2.39240.27371420.19912464X-RAY DIFFRACTION100
2.3924-2.51850.25561370.20852505X-RAY DIFFRACTION100
2.5185-2.67630.2421400.20622483X-RAY DIFFRACTION100
2.6763-2.88280.25761330.21212490X-RAY DIFFRACTION100
2.8828-3.17280.27031440.20242522X-RAY DIFFRACTION100
3.1728-3.63150.23761470.18362489X-RAY DIFFRACTION100
3.6315-4.57380.19031360.15432524X-RAY DIFFRACTION100
4.5738-35.39770.18571400.17922547X-RAY DIFFRACTION99

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