5XXV

GDP-microtubule complexed with KIF5C in AMPPNP state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.46 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Kinesin-binding-triggered conformation switching of microtubules contributes to polarized transport

Shima, T.Morikawa, M.Kaneshiro, J.Kambara, T.Kamimura, S.Yagi, T.Iwamoto, H.Uemura, S.Shigematsu, H.Shirouzu, M.Ichimura, T.Watanabe, T.M.Nitta, R.Okada, Y.Hirokawa, N.

(2018) J. Cell Biol. 217: 4164-4183

  • DOI: 10.1083/jcb.201711178
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Kinesin-1, the founding member of the kinesin superfamily of proteins, is known to use only a subset of microtubules for transport in living cells. This biased use of microtubules is proposed as the guidance cue for polarized transport in neurons, bu ...

    Kinesin-1, the founding member of the kinesin superfamily of proteins, is known to use only a subset of microtubules for transport in living cells. This biased use of microtubules is proposed as the guidance cue for polarized transport in neurons, but the underlying mechanisms are still poorly understood. Here, we report that kinesin-1 binding changes the microtubule lattice and promotes further kinesin-1 binding. This high-affinity state requires the binding of kinesin-1 in the nucleotide-free state. Microtubules return to the initial low-affinity state by washing out the binding kinesin-1 or by the binding of non-hydrolyzable ATP analogue AMPPNP to kinesin-1. X-ray fiber diffraction, fluorescence speckle microscopy, and second-harmonic generation microscopy, as well as cryo-EM, collectively demonstrated that the binding of nucleotide-free kinesin-1 to GDP microtubules changes the conformation of the GDP microtubule to a conformation resembling the GTP microtubule.


    Organizational Affiliation

    Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan hirokawa@m.u-tokyo.ac.jp.,Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Hyogo, Japan.,Department of Physics, Universal Biology Institute and the International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan.,Center of Excellence in Genome Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan.,Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan.,Department of Life Sciences, Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Hiroshima, Japan.,Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan.,Life and Environmental Division, SPring-8, Japan Synchrotron Radiation Research Institute, Hyogo, Japan.,Structural Biology Group, RIKEN Center for Biosystems Dynamics Research, Kanagawa, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan y.okada@riken.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1A chain
A, C, E, G, I, K, M, O, Q
438Sus scrofaMutation(s): 0 
Gene Names: TUBA1A
Find proteins for P02550 (Sus scrofa)
Go to Gene View: TUBA1A
Go to UniProtKB:  P02550
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta chain
B, D, F, H, J, L, N, P, R
426Sus scrofaMutation(s): 0 
Find proteins for P02554 (Sus scrofa)
Go to UniProtKB:  P02554
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
B, D, F, H, J, L, N, P, R
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
B, D, F, H, J, L, N, P, R
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O, Q
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.46 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan23000013
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan16H06372
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan17H05897
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan15K08168

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references, Structure summary
  • Version 1.2: 2018-12-19
    Type: Data collection, Database references