7TR2

Apo CaKip3[2-436]-L2-mutant(HsKHC) in complex with a microtubule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Kinesin-8-specific loop-2 controls the dual activities of the motor domain according to tubulin protofilament shape.

Hunter, B.Benoit, M.P.M.H.Asenjo, A.B.Doubleday, C.Trofimova, D.Frazer, C.Shoukat, I.Sosa, H.Allingham, J.S.

(2022) Nat Commun 13: 4198-4198

  • DOI: https://doi.org/10.1038/s41467-022-31794-3
  • Primary Citation of Related Structures:  
    7LFF, 7TQX, 7TQY, 7TQZ, 7TR0, 7TR1, 7TR2, 7TR3

  • PubMed Abstract: 

    Kinesin-8s are dual-activity motor proteins that can move processively on microtubules and depolymerize microtubule plus-ends, but their mechanism of combining these distinct activities remains unclear. We addressed this by obtaining cryo-EM structures (2.6-3.9 Å) of Candida albicans Kip3 in different catalytic states on the microtubule lattice and on a curved microtubule end mimic. We also determined a crystal structure of microtubule-unbound CaKip3-ADP (2.0 Å) and analyzed the biochemical activity of CaKip3 and kinesin-1 mutants. These data reveal that the microtubule depolymerization activity of kinesin-8 originates from conformational changes of its motor core that are amplified by dynamic contacts between its extended loop-2 and tubulin. On curved microtubule ends, loop-1 inserts into preceding motor domains, forming head-to-tail arrays of kinesin-8s that complement loop-2 contacts with curved tubulin and assist depolymerization. On straight tubulin protofilaments in the microtubule lattice, loop-2-tubulin contacts inhibit conformational changes in the motor core, but in the ADP-Pi state these contacts are relaxed, allowing neck-linker docking for motility. We propose that these tubulin shape-induced alternations between pro-microtubule-depolymerization and pro-motility kinesin states, regulated by loop-2, are the key to the dual activity of kinesin-8 motors.


  • Organizational Affiliation

    Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein,Kinesin-1 heavy chainA [auth K]420Candida albicansHomo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for C4YNU9 (Candida albicans (strain WO-1))
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Go to UniProtKB:  C4YNU9
Find proteins for P33176 (Homo sapiens)
Explore P33176 
Go to UniProtKB:  P33176
PHAROS:  P33176
GTEx:  ENSG00000170759 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP33176C4YNU9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chainB [auth A]451Sus scrofaMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa)
Explore Q2XVP4 
Go to UniProtKB:  Q2XVP4
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UniProt GroupQ2XVP4
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-2B chainC [auth B]445Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
Entity Groups  
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UniProt GroupP02554
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM113164
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN/356025-2013
Canadian Institutes of Health Research (CIHR)CanadaMOP-97832

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references
  • Version 1.2: 2024-02-21
    Changes: Data collection