9E0W | pdb_00009e0w

Cryo-EM structure of human cytoplasmic dynein-1 bound to LIS1 in the presence of ATP


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 1.1 of the entry. See complete history


Literature

Cryo-EM captures early intermediate steps in dynein activation by LIS1.

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

(2025) Nat Commun 16: 7054-7054

  • DOI: https://doi.org/10.1038/s41467-025-62185-z
  • Primary Citation of Related Structures:  
    9DZY, 9E0K, 9E0T, 9E0U, 9E0W, 9E0X, 9E0Y, 9E22, 9E23, 9E28

  • PubMed Abstract: 

    Cytoplasmic dynein-1 (dynein) is an essential molecular motor in eukaryotic cells. Dynein primarily exists in an autoinhibited Phi state and requires conformational changes to assemble with its cofactors and form active transport complexes. LIS1, a key dynein regulator, enhances dynein activation and assembly. Using cryo-EM and a human dynein-LIS1 sample incubated with ATP, we map the conformational landscape of dynein activation by LIS1 and identify an early intermediate state that we propose precedes the previously identified dynein-LIS1 Chi state. Mutations that disrupt this species, which we termed "Pre-Chi", lead to motility defects in vitro, emphasizing its functional importance. Together, our findings provide insights into how LIS1 relieves dynein autoinhibition during the activation pathway.


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

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic dynein 1 heavy chain 14,843Homo 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Platelet-activating factor acetylhydrolase IB subunit betaB [auth C]411Homo sapiensMutation(s): 0 
Gene Names: PAFAH1B1LIS1MDCRMDSPAFAHA
UniProt & NIH Common Fund Data Resources
Find proteins for P43034 (Homo sapiens)
Explore P43034 
Go to UniProtKB:  P43034
PHAROS:  P43034
GTEx:  ENSG00000007168 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43034
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
D [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
F [auth A],
G [auth A]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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

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 StatesT32 GM139795
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM145296

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2026-01-21
    Changes: Data collection, Database references