9BMN | pdb_00009bmn

State-5 of motor domain from full-length human dynein-1 in 5mM AMPPNP

  • Classification: MOTOR PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Spodoptera frugiperda
  • Mutation(s): No 

  • Deposited: 2024-05-02 Released: 2025-04-23 
  • Deposition Author(s): Chai, P., Zhang, K.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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

The mechanochemical cycle of reactive full-length human dynein 1.

Chai, P.Yang, J.Geohring, I.C.Markus, S.M.Wang, Y.Zhang, K.

(2025) Nat Struct Mol Biol 32: 1383-1395

  • DOI: https://doi.org/10.1038/s41594-025-01543-3
  • Primary Citation of Related Structures:  
    9BLY, 9BLZ, 9BM0, 9BM1, 9BM2, 9BM3, 9BM4, 9BM5, 9BM6, 9BM7, 9BM8, 9BMA, 9BMB, 9BMC, 9BMD, 9BMF, 9BMG, 9BMH, 9BMJ, 9BML, 9BMM, 9BMN, 9BMO, 9BMP, 9BMR, 9BMS, 9BMT, 9BMU, 9BMV, 9BMW, 9BMY, 9BMZ, 9BN0, 9BN1, 9BN3, 9BN4, 9BN5, 9BN6, 9DH5, 9DH6, 9DH7, 9DH8, 9DH9, 9DHA

  • PubMed Abstract: 

    Dynein-driven cargo transport has a pivotal role in diverse cellular activities, central to which is dynein's mechanochemical cycle. Here, we performed a systematic cryo-electron microscopic investigation of the conformational landscape of full-length human dynein 1 in reaction, in various nucleotide conditions, on and off microtubules. Our approach reveals over 40 high-resolution structures, categorized into eight states, providing a dynamic and comprehensive view of dynein throughout its mechanochemical cycle. The described intermediate states reveal mechanistic insights into dynein function, including a 'backdoor' phosphate release model that coordinates linker straightening, how microtubule binding enhances adenosine triphosphatase activity through a two-way communication mechanism and the crosstalk mechanism between AAA1 and the regulatory AAA3 site. Our findings also lead to a revised model for the force-generating powerstroke and reveal means by which dynein exhibits unidirectional stepping. These results improve our understanding of dynein and provide a more complete model of its mechanochemical cycle.


  • Organizational Affiliation
    • Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic dynein 1 heavy chain 14,646Homo sapiensMutation(s): 0 
Gene Names: DYNC1H1DHC1DNCH1DNCLDNECLDYHCKIAA0325
UniProt & NIH Common Fund Data Resources
Find proteins for Q14204 (Homo sapiens)
Explore Q14204 
Go to UniProtKB:  Q14204
PHAROS:  Q14204
GTEx:  ENSG00000197102 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14204
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
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 StatesR35GM142959
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM139483

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Data collection, Database references
  • Version 1.2: 2025-08-27
    Changes: Data collection, Database references