9E0K | pdb_00009e0k

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

• PDB DOI: https://doi.org/10.2210/pdb9E0K/pdb
• EM Map EMD-47360: EMDB EMDataResource

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


• Deposited: 2024-10-18 Released: 2025-07-09 
• Deposition Author(s): Nguyen, K.H.V., Kendrick, A.A., Leschziner, A.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

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

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

• PubMed: 40750582 
• 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.

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Organizational Affiliation: 
• Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Salk Institute for Biological Studies, La Jolla, CA, USA.
Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA. [e-mail].
Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA. [e-mail].
Howard Hughes Medical Institute, Chevy Chase, MD, USA. [e-mail].
Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA. [e-mail].
Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 555.96 kDa 
• Atom Count: 22,930 
• Modeled Residue Count: 2,892 
• Deposited Residue Count: 4,843 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoplasmic dynein 1 heavy chain 1	A	4,843	Homo sapiens	Mutation(s): 0  Gene Names: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325
UniProt & NIH Common Fund Data Resources
Find proteins for Q14204 (Homo sapiens) Explore Q14204  Go to UniProtKB:  Q14204
PHAROS:  Q14204 GTEx:  ENSG00000197102

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	D [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)	B [auth A], F [auth A], G [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	C [auth A], E [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:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Nguyen, K.H.V., Kendrick, A.A., Leschziner, A.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM139795
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM145296

Revision History  

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