3J6H

Nucleotide-free Kinesin motor domain complexed with GMPCPP-microtubule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-ray and Cryo-EM structures reveal mutual conformational changes of Kinesin and GTP-state microtubules upon binding

Morikawa, M.Yajima, H.Nitta, R.Inoue, S.Ogura, T.Sato, C.Hirokawa, N.

(2015) EMBO J 

  • DOI: https://doi.org/10.15252/embj.201490588
  • Primary Citation of Related Structures:  
    3J6H, 3WRD, 3X2T

  • PubMed Abstract: 

    The molecular motor kinesin moves along microtubules using energy from ATP hydrolysis in an initial step coupled with ADP release. In neurons, kinesin-1/KIF5C preferentially binds to the GTP-state microtubules over GDP-state microtubules to selectively enter an axon among many processes; however, because the atomic structure of nucleotide-free KIF5C is unavailable, its molecular mechanism remains unresolved. Here, the crystal structure of nucleotide-free KIF5C and the cryo-electron microscopic structure of nucleotide-free KIF5C complexed with the GTP-state microtubule are presented. The structures illustrate mutual conformational changes induced by interaction between the GTP-state microtubule and KIF5C. KIF5C acquires the 'rigor conformation', where mobile switches I and II are stabilized through L11 and the initial portion of the neck-linker, facilitating effective ADP release and the weak-to-strong transition of KIF5C microtubule affinity. Conformational changes to tubulin strengthen the longitudinal contacts of the GTP-state microtubule in a similar manner to GDP-taxol microtubules. These results and functional analyses provide the molecular mechanism of the preferential binding of KIF5C to GTP-state microtubules.


  • Organizational Affiliation

    Department of Cell Biology and Anatomy, The University of Tokyo, Hongo Tokyo, Japan Department of Molecular Structure and Dynamics, Graduate School of Medicine, The University of Tokyo, Hongo Tokyo, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1A chain436Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02550 (Sus scrofa)
Explore P02550 
Go to UniProtKB:  P02550
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UniProt GroupP02550
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain426Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
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UniProt GroupP02554
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin heavy chain isoform 5CC [auth K]352Mus musculusMutation(s): 0 
Gene Names: Kif5c
UniProt & NIH Common Fund Data Resources
Find proteins for P28738 (Mus musculus)
Explore P28738 
Go to UniProtKB:  P28738
IMPC:  MGI:1098269
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UniProt GroupP28738
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONIMAGIC5
RECONSTRUCTIONMATLAB

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Refinement description