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 1.2 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: 10.1016/j.celrep.2017.08.067
  • Primary Citation of Related Structures:  
    5XJB, 5XJA

  • 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 ...

    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; Center of Excellence in Genome Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia. Electronic address: hirokawa@m.u-tokyo.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-like protein KIF2CA, B426Mus 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
AF3
Query on AF3

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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