8YUE | pdb_00008yue

Crystal structure of the kinesin-14 motor protein from Drosophila melanogaster


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 
    0.295 (Depositor), 0.317 (DCC) 
  • R-Value Work: 
    0.251 (Depositor), 0.276 (DCC) 
  • R-Value Observed: 
    0.253 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural analysis of a motor with increased mechanical output reveals new transitions in kinesin microtubule motility.

Shibata, S.Wang, M.Y.Imasaki, T.Shigematsu, H.Ugarte La Torre, D.Wei, Y.Jobichen, C.Hagio, H.Sivaraman, J.Sugita, Y.Endow, S.A.Nitta, R.

(2026) Sci Rep 16: 487-487

  • DOI: https://doi.org/10.1038/s41598-025-28573-7
  • Primary Citation Related Structures: 
    8YUE, 8YY2, 8YY3, 8YY4, 8YY5

  • PubMed Abstract: 

    Kinesin motors use ATP to produce force in cells, yet the conformational changes that generate force remain uncertain. Here, we report structural and mechanistic insights into a minus-end-directed kinesin-14 that exhibits increased mechanical output – the variant motor binds microtubules more tightly and moves with faster velocity than wild type. High-resolution structures, together with molecular dynamics simulations, reveal previously unobserved transitions in the nucleotide hydrolysis cycle. ADP release, triggered by microtubule binding, is coupled to twisting of the central β-sheet and stabilization of the stalk prior to the power stroke. ATP binding induces stalk fluctuations and a swing of the neck mimic, an element analogous to the kinesin-1 neck linker, resembling neck linker docking in plus-end-directed kinesins. The power stroke, characterized by a large stalk rotation, is followed by motor detachment from microtubules. The subsequent recovery stroke occurs while the motor is bound to ADP and free Pi, accompanied by β-strand-to-loop transitions, or β-sheet melting, implying that β-sheet refolding facilitates Pi release. The observed twisting and melting identify the central β-sheet as the long-sought elastic element or spring required for motor force production. The transitions we observe in kinesin-14 may also apply to other kinesins – this remains to be tested. The online version contains supplementary material available at 10.1038/s41598-025-28573-7.


  • Organizational Affiliation
    • Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, 650-0017, Kobe, Japan.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein claret segregational
A, B
390Drosophila melanogasterMutation(s): 1 
Gene Names: ncdCA(ND)CG7831
EC: 3.6.4
UniProt
Find proteins for P20480 (Drosophila melanogaster)
Explore P20480 
Go to UniProtKB:  P20480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20480
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free:  0.295 (Depositor), 0.317 (DCC) 
  • R-Value Work:  0.251 (Depositor), 0.276 (DCC) 
  • R-Value Observed: 0.253 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.506α = 90
b = 67.617β = 96.99
c = 94.196γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United States1R21HD105034-01A1

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Database references