[English] 日本語
Yorodumi
- PDB-5dms: Mouse Polo-box domain and Emi2 (169-177) -

+
Open data


ID or keywords:

Loading...

-
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 / Golgi Cisternae Pericentriolar Stack Reorganization / negative regulation of cell cycle process / Mitotic Telophase/Cytokinesis / meiotic nuclear division / Cyclin A/B1/B2 associated events during G2/M transition ...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 / negative regulation of cell cycle process / Mitotic Telophase/Cytokinesis / meiotic nuclear division / 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 / 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 / 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 / regulation of meiotic nuclear division / synaptonemal complex disassembly / The role of GTSE1 in G2/M progression after G2 checkpoint / RHO GTPases Activate Formins / nuclear membrane disassembly / homologous chromosome segregation / Separation of Sister Chromatids / polo kinase / 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 / Regulation of PLK1 Activity at G2/M Transition / synaptonemal complex / female meiosis chromosome segregation / anaphase-promoting complex binding / outer kinetochore / condensed chromosome, centromeric region / positive regulation of ubiquitin protein ligase activity / double-strand break repair via alternative nonhomologous end joining / regulation of mitotic spindle assembly / microtubule bundle formation / female germ cell nucleus / centrosome cycle / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic nuclear division / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / mitotic G2 DNA damage checkpoint signaling / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / mitotic cytokinesis / chromosome, centromeric region / centriolar satellite / spindle midzone / negative regulation of double-strand break repair via homologous recombination / protein localization to chromatin / centriole / mitotic spindle organization / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule / establishment of protein localization / protein catabolic process / negative regulation of protein catabolic process / protein destabilization / kinetochore / spindle pole / spindle / G2/M transition of mitotic cell cycle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / microtubule binding / 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 / zinc ion binding / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
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 ...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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more