5VH9

Cryo-EM structure of yeast cytoplasmic dynein-1 with Lis1 and ATP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Lis1 Has Two Opposing Modes of Regulating Cytoplasmic Dynein.

DeSantis, M.E.Cianfrocco, M.A.Htet, Z.M.Tran, P.T.Reck-Peterson, S.L.Leschziner, A.E.

(2017) Cell 170: 1197-1208.e12

  • DOI: https://doi.org/10.1016/j.cell.2017.08.037
  • Primary Citation of Related Structures:  
    5VH9, 5VLJ

  • PubMed Abstract: 

    Regulation is central to the functional versatility of cytoplasmic dynein, a motor involved in intracellular transport, cell division, and neurodevelopment. Previous work established that Lis1, a conserved regulator of dynein, binds to its motor domain and induces a tight microtubule-binding state in dynein. The work we present here-a combination of biochemistry, single-molecule assays, and cryoelectron microscopy-led to the surprising discovery that Lis1 has two opposing modes of regulating dynein, being capable of inducing both low and high affinity for the microtubule. We show that these opposing modes depend on the stoichiometry of Lis1 binding to dynein and that this stoichiometry is regulated by the nucleotide state of dynein's AAA3 domain. The low-affinity state requires Lis1 to also bind to dynein at a novel conserved site, mutation of which disrupts Lis1's function in vivo. We propose a new model for the regulation of dynein by Lis1.


  • Organizational Affiliation

    Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein heavy chain, cytoplasmic2,376Saccharomyces 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear distribution protein PAC1354Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PAC1LIS1SCY_5321
UniProt
Find proteins for A6ZPA6 (Saccharomyces cerevisiae (strain YJM789))
Explore A6ZPA6 
Go to UniProtKB:  A6ZPA6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6ZPA6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta3.7

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM107214
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM100947

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence