9E11 image
Deposition Date 2024-10-21
Release Date 2025-08-06
Last Version Date 2025-08-13
Entry Detail
PDB ID:
9E11
Keywords:
Title:
Dimeric motor domains from phi-like dynein-1 bound to a Lis1 dimer under Lis1 condition
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.86 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytoplasmic dynein 1 heavy chain 1
Gene (Uniprot):DYNC1H1
Chain IDs:A, B
Chain Length:4646
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Platelet-activating factor acetylhydrolase IB subunit beta
Gene (Uniprot):PAFAH1B1
Chain IDs:C, D
Chain Length:410
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Nde1 promotes Lis1 binding to full-length autoinhibited human dynein 1.
Nat.Chem.Biol. ? ? ? (2025)
PMID: 40751002 DOI: 10.1038/s41589-025-01981-6

Abstact

Cytoplasmic dynein 1 (dynein) is the primary motor responsible for the retrograde transport of intracellular cargoes along microtubules. Activation of dynein requires the opening its autoinhibited Phi conformation, a process driven by Lis1 and Nde1/Ndel1. Using biochemical reconstitution and cryo-electron microscopy, we demonstrate that Nde1 enhances Lis1 binding to autoinhibited dynein and facilitates Phi opening. We identify a key intermediate in this activation pathway where a single Lis1 dimer binds between Phi-like (PhiL) motor rings. In this 'PhiL-Lis1' complex, Lis1 interacts with one motor domain through canonical sites at the AAA+ (adenosine triphosphatases associated with diverse cellular activities) ring and stalk, and with AAA5, AAA6 and linker regions of the other motor domain. Mutagenesis and motility assays confirm the critical role of the PhiL-Lis1 interface in dynein activation. This intermediate forms rapidly in the presence of Nde1, although Nde1 is not part of PhiL-Lis1. These findings provide key insights into how Nde1 promotes Lis1-mediated Phi opening.

Legend

Protein

Chemical

Disease

Primary Citation of related structures