5XJA

The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with ADP-Mg-AlFx


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

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This is version 1.3 of the entry. See complete history


Literature

Mechanism of Catalytic Microtubule Depolymerization via KIF2-Tubulin Transitional Conformation

Ogawa, T.Saijo, S.Shimizu, N.Jiang, X.Hirokawa, N.

(2017) Cell Rep 20: 2626-2638

  • DOI: https://doi.org/10.1016/j.celrep.2017.08.067
  • Primary Citation of Related Structures:  
    5XJA, 5XJB

  • PubMed Abstract: 

    Microtubules (MTs) are dynamic structures that are fundamental for cell morphogenesis and motility. MT-associated motors work efficiently to perform their functions. Unlike other motile kinesins, KIF2 catalytically depolymerizes MTs from the peeled protofilament end during ATP hydrolysis. However, the detailed mechanism by which KIF2 drives processive MT depolymerization remains unknown. To elucidate the catalytic mechanism, the transitional KIF2-tubulin complex during MT depolymerization was analyzed through multiple methods, including atomic force microscopy, size-exclusion chromatography, multi-angle light scattering, small-angle X-ray scattering, analytical ultracentrifugation, and mass spectrometry. The analyses outlined the conformation in which one KIF2core domain binds tightly to two tubulin dimers in the middle pre-hydrolysis state during ATP hydrolysis, a process critical for catalytic MT depolymerization. The X-ray crystallographic structure of the KIF2core domain displays the activated conformation that sustains the large KIF2-tubulin 1:2 complex.


  • Organizational Affiliation

    Department of Cell Biology and Anatomy, University of Tokyo, Graduate School of Medicine Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein KIF2C
A, B
426Mus musculusMutation(s): 0 
Gene Names: Kif2c
UniProt & NIH Common Fund Data Resources
Find proteins for Q922S8 (Mus musculus)
Explore Q922S8 
Go to UniProtKB:  Q922S8
IMPC:  MGI:1921054
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ922S8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.098α = 90
b = 166.989β = 90
c = 74.991γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan23000013, 16H06372

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Database references
  • Version 1.2: 2017-10-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description