[English] 日本語
Yorodumi
- PDB-5nd3: Microtubule-bound MKLP2 motor domain in the with no nucleotide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nd3
TitleMicrotubule-bound MKLP2 motor domain in the with no nucleotide
Components
  • Kinesin-like protein KIF20A
  • Tubulin alpha chain
  • Tubulin beta-2B chain
KeywordsMOTOR PROTEIN / Kinesin Mitosis Microtubules
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation ...Mitotic Telophase/Cytokinesis / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / COPI-dependent Golgi-to-ER retrograde traffic / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Kinesins / MHC class II antigen presentation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Aggrephagy / COPI-dependent Golgi-to-ER retrograde traffic / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of NuMA to mitotic centrosomes / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / midbody abscission / MHC class II antigen presentation / microtubule bundle formation / positive regulation of axon guidance / microtubule motor activity / microtubule-based movement / cleavage furrow / mitotic cytokinesis / microtubule-based process / intercellular bridge / cytoplasmic microtubule / cellular response to interleukin-4 / regulation of cytokinesis / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / neuron migration / mitotic spindle / protein transport / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / midbody / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / cilium / protein heterodimerization activity / GTPase activity / ubiquitin protein ligase binding / protein kinase binding / GTP binding / Golgi apparatus / nucleoplasm / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. ...: / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOL / Tubulin alpha chain / Tubulin alpha-1B chain / Kinesin-like protein KIF20A / Tubulin beta-2B chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsAtherton, J. / Yu, I.M. / Cook, A. / Muretta, J.M. / Joseph, A.P. / Major, J. / Sourigues, Y. / Clause, J. / Topf, M. / Rosenfeld, S.S. ...Atherton, J. / Yu, I.M. / Cook, A. / Muretta, J.M. / Joseph, A.P. / Major, J. / Sourigues, Y. / Clause, J. / Topf, M. / Rosenfeld, S.S. / Houdusse, A. / Moores, C.A.
Funding support United Kingdom, United States, 13items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/J000973/1 United Kingdom
Medical Research Council (United Kingdom)MR/J003867/1 United Kingdom
Medical Research Council (United Kingdom)MR/M019292/1 United Kingdom
American Heart AssociationSDG20480032 United States
National Institutes of HealthGM102875 United States
National Institutes of HealthNS073610 United States
CNRSANR-15-CE13-0017-01
Instruct-pilote, Ligue Contre le CancerRS14/75-28
ARCPJA 20151203285
INCa2016-1-PL BIO-10-ICR-1
Marie Curie FellowshipFP7-PEOPLE-2012-IIF
Labex CelTisPhyBio11-LBX-0038
PSL Research UniversityANR-10-IDEX-0001-02 PSL
CitationJournal: Elife / Year: 2017
Title: The divergent mitotic kinesin MKLP2 exhibits atypical structure and mechanochemistry.
Authors: Joseph Atherton / I-Mei Yu / Alexander Cook / Joseph M Muretta / Agnel Joseph / Jennifer Major / Yannick Sourigues / Jeffrey Clause / Maya Topf / Steven S Rosenfeld / Anne Houdusse / Carolyn A Moores /
Abstract: MKLP2, a kinesin-6, has critical roles during the metaphase-anaphase transition and cytokinesis. Its motor domain contains conserved nucleotide binding motifs, but is divergent in sequence (~35% ...MKLP2, a kinesin-6, has critical roles during the metaphase-anaphase transition and cytokinesis. Its motor domain contains conserved nucleotide binding motifs, but is divergent in sequence (~35% identity) and size (~40% larger) compared to other kinesins. Using cryo-electron microscopy and biophysical assays, we have undertaken a mechanochemical dissection of the microtubule-bound MKLP2 motor domain during its ATPase cycle, and show that many facets of its mechanism are distinct from other kinesins. While the MKLP2 neck-linker is directed towards the microtubule plus-end in an ATP-like state, it does not fully dock along the motor domain. Furthermore, the footprint of the MKLP2 motor domain on the MT surface is altered compared to motile kinesins, and enhanced by kinesin-6-specific sequences. The conformation of the highly extended loop6 insertion characteristic of kinesin-6s is nucleotide-independent and does not contact the MT surface. Our results emphasize the role of family-specific insertions in modulating kinesin motor function.
History
DepositionMar 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.0Oct 4, 2017Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 4, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 4, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: database_2 / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.2Oct 1, 2025Group: Advisory / Data collection / Derived calculations
Category: em_admin / pdbx_validate_close_contact ...em_admin / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update
Revision 1.2Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-3621
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3621
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Kinesin-like protein KIF20A
A: Tubulin alpha chain
B: Tubulin beta-2B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,8817
Polymers156,0363
Non-polymers1,8454
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9370 Å2
ΔGint-50 kcal/mol
Surface area43610 Å2
MethodPISA
Number of models5

-
Components

-
Protein , 3 types, 3 molecules CAB

#1: Protein Kinesin-like protein KIF20A / Kinesin-like protein 174 / Rab6-interacting kinesin-like protein / Rabkinesin-6


Mass: 56021.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif20a, Rab6kifl / Production host: Escherichia coli (E. coli) / References: UniProt: P97329
#2: Protein Tubulin alpha chain


Mass: 50107.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: F2Z4C1, UniProt: P81947*PLUS
#3: Protein Tubulin beta-2B chain


Mass: 49907.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q6B856

-
Non-polymers , 4 types, 4 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication*YM

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Complex of 13pf taxol-GDP microtubule with bound MKLP2 motor domain with no-nucleotideCOMPLEXMicrotubule bound to taxol and GDP#1-#30MULTIPLE SOURCES
2Kinesin-like protein KIF20ACOMPLEXMicrotubule bound to taxol and GDP#11RECOMBINANT
3Tubulin alpha and beta chainsCOMPLEXMicrotubule bound to taxol and GDP#2-#31NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Mus musculus (house mouse)10090
23Bos taurus (domestic cattle)9913
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9257
Details: Gold-standard FSCtrue using noise substitution test (Chen et al., 2014)
Symmetry type: POINT

+
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