9E12 image
Deposition Date 2024-10-21
Release Date 2025-08-06
Last Version Date 2025-08-13
Entry Detail
PDB ID:
9E12
Keywords:
Title:
Full-length human dynein-1 in phi comformation under Lis1 condition
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
4.50 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:Cytoplasmic dynein 1 intermediate chain 2
Gene (Uniprot):DYNC1I2
Chain IDs:C, D
Chain Length:638
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytoplasmic dynein 1 light intermediate chain 2
Gene (Uniprot):DYNC1LI2
Chain IDs:E, F
Chain Length:492
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Dynein light chain roadblock-type 1
Gene (Uniprot):DYNLRB1
Chain IDs:G, H
Chain Length:96
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Dynein light chain 1, cytoplasmic
Gene (Uniprot):DYNLL1
Chain IDs:I, J
Chain Length:89
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Dynein light chain Tctex-type 1
Gene (Uniprot):DYNLT1
Chain IDs:K, L
Chain Length:113
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.

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Primary Citation of related structures