9DNB | pdb_00009dnb

CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Multiple steps of dynein activation by Lis1 visualized by cryo-EM.

Kendrick, A.A.Nguyen, K.H.V.Ma, W.Karasmanis, E.P.Amaro, R.E.Reck-Peterson, S.L.Leschziner, A.E.

(2025) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-025-01558-w
  • Primary Citation of Related Structures:  
    9DI3, 9DIU, 9DJ7, 9DJU, 9DJY, 9DJZ, 9DK0, 9DKD, 9DKE, 9DKH, 9DKJ, 9DKM, 9DKX, 9DLD, 9DLE, 9DMW, 9DN5, 9DN7, 9DNB

  • PubMed Abstract: 

    Cytoplasmic dynein-1 (dynein) is an essential molecular motor controlled in part by autoinhibition. Lis1, a key dynein regulator mutated in the neurodevelopmental disease lissencephaly, plays a role in dynein activation. We recently identified a structure of partially autoinhibited dynein bound to Lis1, which suggests an intermediate state in dynein's activation pathway. However, other structural information is needed to fully understand how Lis1 activates dynein. Here, we used cryo-EM and yeast dynein and Lis1 incubated with ATP at different time points to reveal conformations that we propose represent additional intermediate states in dynein's activation pathway. We solved 16 high-resolution structures, including 7 distinct dynein and dynein-Lis1 structures from the same sample. Our data support a model in which Lis1 relieves dynein autoinhibition by increasing its basal ATP hydrolysis rate and promoting conformations compatible with complex assembly and motility. Together, this analysis advances our understanding of dynein activation and the contribution of Lis1 to this process.


  • Organizational Affiliation

    Salk Institute for Biological Studies, La Jolla, CA, USA. akendrick@salk.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein heavy chain, cytoplasmic2,875Saccharomyces cerevisiaeMutation(s): 0 
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear distribution protein PAC1
B, C
495Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PAC1LIS1YOR269W
UniProt
Find proteins for P39946 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39946 
Go to UniProtKB:  P39946
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39946
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release