5ND4

Microtubule-bound MKLP2 motor domain in the presence of ADP.AlFx


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The divergent mitotic kinesin MKLP2 exhibits atypical structure and mechanochemistry.

Atherton, J.Yu, I.M.Cook, A.Muretta, J.M.Joseph, A.Major, J.Sourigues, Y.Clause, J.Topf, M.Rosenfeld, S.S.Houdusse, A.Moores, C.A.

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.27793
  • Primary Citation of Related Structures:  
    5ND2, 5ND3, 5ND4, 5ND7

  • PubMed 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% 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.


  • Organizational Affiliation

    Institute of Structural and Molecular Biology, Birkbeck College, London, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein KIF20AA [auth C]501Mus musculusMutation(s): 0 
Gene Names: Kif20aRab6kifl
UniProt & NIH Common Fund Data Resources
Find proteins for P97329 (Mus musculus)
Explore P97329 
Go to UniProtKB:  P97329
IMPC:  MGI:1201682
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97329
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha chainB [auth A]412Bos taurusMutation(s): 0 
UniProt
Find proteins for P81947 (Bos taurus)
Explore P81947 
Go to UniProtKB:  P81947
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81947
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-2B chainC [auth B]426Bos taurusMutation(s): 0 
UniProt
Find proteins for Q6B856 (Bos taurus)
Explore Q6B856 
Go to UniProtKB:  Q6B856
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6B856
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TA1
Query on TA1

Download Ideal Coordinates CCD File 
J [auth B]TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N
GTP
Query on GTP

Download Ideal Coordinates CCD File 
G [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
I [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
D [auth C]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ALF
Query on ALF

Download Ideal Coordinates CCD File 
F [auth C]TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth C],
H [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TA1 BindingDB:  5ND4 EC50: 520 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/J000973/1
Medical Research Council (United Kingdom)United KingdomMR/J003867/1
Medical Research Council (United Kingdom)United KingdomMR/M019292/1
American Heart AssociationUnited StatesSDG20480032
National Institutes of HealthUnited StatesGM102875
National Institutes of HealthUnited StatesNS073610
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

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-04
    Type: Initial release