9E13 | pdb_00009e13

Full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Lis1 condition

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

  • Deposited: 2024-10-21 Released: 2025-08-06 
  • Deposition Author(s): Yang, J., Zhang, K.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 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

Nde1 promotes Lis1 binding to full-length autoinhibited human dynein 1.

Yang, J.Zhao, Y.Chai, P.Yildiz, A.Zhang, K.

(2025) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-025-01981-6
  • Primary Citation of Related Structures:  
    9E0Z, 9E10, 9E11, 9E12, 9E13, 9E14

  • PubMed Abstract: 

    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 (Phi L ) motor rings. In this 'Phi L -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 Phi L -Lis1 interface in dynein activation. This intermediate forms rapidly in the presence of Nde1, although Nde1 is not part of Phi L -Lis1. These findings provide key insights into how Nde1 promotes Lis1-mediated Phi opening.


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

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic dynein 1 heavy chain 1
A, B
4,646Homo sapiensMutation(s): 0 
Gene Names: DYNC1H1DHC1DNCH1DNCLDNECLDYHCKIAA0325
UniProt & NIH Common Fund Data Resources
Find proteins for Q14204 (Homo sapiens)
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PHAROS:  Q14204
GTEx:  ENSG00000197102 
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UniProt GroupQ14204
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic dynein 1 intermediate chain 2
C, D
638Homo sapiensMutation(s): 0 
Gene Names: DYNC1I2DNCI2DNCIC2
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Find proteins for Q13409 (Homo sapiens)
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PHAROS:  Q13409
GTEx:  ENSG00000077380 
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UniProt GroupQ13409
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic dynein 1 light intermediate chain 2
E, F
492Homo sapiensMutation(s): 0 
Gene Names: DYNC1LI2DNCLI2LIC2
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Find proteins for O43237 (Homo sapiens)
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PHAROS:  O43237
GTEx:  ENSG00000135720 
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UniProt GroupO43237
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain roadblock-type 1
G, H
96Homo sapiensMutation(s): 0 
Gene Names: DYNLRB1BITHDNCL2ADNLC2AROBLD1HSPC162
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Find proteins for Q9NP97 (Homo sapiens)
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GTEx:  ENSG00000125971 
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UniProt GroupQ9NP97
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain 1, cytoplasmic
I, J
89Homo sapiensMutation(s): 0 
Gene Names: DYNLL1DLC1DNCL1DNCLC1HDLC1
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Find proteins for P63167 (Homo sapiens)
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GTEx:  ENSG00000088986 
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UniProt GroupP63167
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain Tctex-type 1
K, L
113Homo sapiensMutation(s): 0 
Gene Names: DYNLT1TCTEL1TCTEX-1TCTEX1
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Find proteins for P63172 (Homo sapiens)
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PHAROS:  P63172
GTEx:  ENSG00000146425 
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UniProt GroupP63172
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Platelet-activating factor acetylhydrolase IB subunit betaM [auth O],
N [auth P]
410Homo sapiensMutation(s): 0 
Gene Names: PAFAH1B1LIS1MDCRMDSPAFAHA
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Find proteins for P43034 (Homo sapiens)
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GTEx:  ENSG00000007168 
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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 
P [auth A],
V [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
O [auth A]
Q [auth A]
R [auth A]
U [auth B]
W [auth B]
O [auth A],
Q [auth A],
R [auth A],
U [auth B],
W [auth B],
X [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
S [auth A],
T [auth A],
Y [auth B],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM142959

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Data collection, Database references