6KJN

The microtubule-binding domains of yeast cytoplasmic dynein in the high affinity state


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for two-way communication between dynein and microtubules.

Nishida, N.Komori, Y.Takarada, O.Watanabe, A.Tamura, S.Kubo, S.Shimada, I.Kikkawa, M.

(2020) Nat Commun 11: 1038-1038

  • DOI: https://doi.org/10.1038/s41467-020-14842-8
  • Primary Citation of Related Structures:  
    6KIO, 6KIQ, 6KJN, 6KJO

  • PubMed Abstract: 

    The movements of cytoplasmic dynein on microtubule (MT) tracks is achieved by two-way communication between the microtubule-binding domain (MTBD) and the ATPase domain via a coiled-coil stalk, but the structural basis of this communication remains elusive. Here, we regulate MTBD either in high-affinity or low-affinity states by introducing a disulfide bond to the stalk and analyze the resulting structures by NMR and cryo-EM. In the MT-unbound state, the affinity changes of MTBD are achieved by sliding of the stalk α-helix by a half-turn, which suggests that structural changes propagate from the ATPase-domain to MTBD. In addition, MT binding induces further sliding of the stalk α-helix even without the disulfide bond, suggesting how the MT-induced conformational changes propagate toward the ATPase domain. Based on differences in the MT-binding surface between the high- and low-affinity states, we propose a potential mechanism for the directional bias of dynein movement on MT tracks.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein heavy chain, cytoplasmic141Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: DYN1DHC1YKR054C
UniProt
Find proteins for P36022 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36022 
Go to UniProtKB:  P36022
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36022
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan26119005
Japan Society for the Promotion of ScienceJapan21121002
Japan Science and TechnologyJapanJPMJCR14M1
Japan Agency for Medical Research and Development (AMED)JapanJP19am01011115

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references, Other
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary