7LFF | pdb_00007lff

Crystal structure of the Candida albicans kinesin-8 motor domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.268 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 99.6 kDa 
  • Atom Count: 5,471 
  • Modeled Residue Count: 663 
  • Deposited Residue Count: 890 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinesin-like protein
A, B
445Candida albicans SC5314Mutation(s): 0 
Gene Names: KIP3orf19.7353CAALFM_C305720CA
UniProt
Find proteins for A0A1D8PKA4 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore A0A1D8PKA4 
Go to UniProtKB:  A0A1D8PKA4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D8PKA4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.268 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.99α = 86.9
b = 52.68β = 79.996
c = 86.75γ = 89.924
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada169149

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description