9MFX | pdb_00009mfx

Motor domain alone with Apo AAA1 and ADP AAA3 from yeast full-length dynein-1 and Pac1 in 0.1 mM ATP condition


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A nucleotide code governs Lis1's ability to relieve dynein autoinhibition.

Geohring, I.C.Chai, P.Iyer, B.R.Ton, W.D.Yang, J.Ide, A.H.George, S.C.Bagri, J.S.Baird, S.V.Zhang, K.Markus, S.M.

(2026) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-025-02096-8
  • Primary Citation of Related Structures:  
    9MFV, 9MFW, 9MFX, 9MFY

  • PubMed Abstract: 

    Dynein-1 is a microtubule motor that transports numerous cytoplasmic cargoes. Activation of motility requires it first overcome an autoinhibited state before its assembly with dynactin and a cargo adaptor. Studies suggest that Lis1 may relieve dynein's autoinhibited state, although evidence for this is lacking. We first determined the rules governing dynein-Lis1 binding, revealing that their binding affinity is regulated by the nucleotide-bound states of each of three nucleotide-binding pockets within dynein. We also found that distinct nucleotide 'codes' coordinate their binding stoichiometry by impacting binding affinity at two different sites within the dynein motor domain. Electron microscopy revealed that a 1 dynein:1 Lis1 complex directly promotes an uninhibited conformational state of dynein, whereas a 1:2 complex resembles the autoinhibited state. Cryo-electron microscopy revealed that the structural basis for Lis1 opening dynein relies on interactions with the linker domain. Our work reveals the biochemical basis by which Lis1 relieves dynein autoinhibition.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein heavy chain, cytoplasmic4,092Saccharomyces 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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4

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 StatesR35 GM139483
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM142959

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Data collection, Database references
  • Version 1.2: 2026-02-04
    Changes: Data collection, Database references