6KIO

Complex of yeast cytoplasmic dynein MTBD-High and MT without DTT


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.94 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/s41467-020-14842-8
  • Structures With Same Primary Citation

  • 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 el ...

    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

    Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. mkikkawa@m.u-tokyo.ac.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta chainb426Sus scrofaMutation(s): 0 
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Dynein heavy chain, cytoplasmicM130Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: DYN1DHC1YKR054C
Find proteins for P36022 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36022 
Go to UniProtKB:  P36022
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1A chaina412Sus scrofaMutation(s): 0 
Gene Names: TUBA1A
Find proteins for P02550 (Sus scrofa)
Explore P02550 
Go to UniProtKB:  P02550
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.94 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJCR14M1
Japan Agency for Medical Research and Development (AMED)JapanJP19am0101115j003

Revision History 

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Database references