9E28 | pdb_00009e28

Cryo-EM structure of Phi dynein tail


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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 1A,
G,
J [auth e],
K [auth f]
4,843Homo 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic dynein 1 light intermediate chain 2
B, C
492Homo sapiensMutation(s): 0 
Gene Names: DYNC1LI2DNCLI2LIC2
UniProt & NIH Common Fund Data Resources
Find proteins for O43237 (Homo sapiens)
Explore O43237 
Go to UniProtKB:  O43237
PHAROS:  O43237
GTEx:  ENSG00000135720 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43237
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2C of Cytoplasmic dynein 1 intermediate chain 2D,
H,
L [auth g],
M [auth h]
612Homo sapiensMutation(s): 0 
Gene Names: DYNC1I2DNCI2DNCIC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13409 (Homo sapiens)
Explore Q13409 
Go to UniProtKB:  Q13409
PHAROS:  Q13409
GTEx:  ENSG00000077380 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13409
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain roadblock-type 1
E, F
96Homo sapiensMutation(s): 0 
Gene Names: DYNLRB1BITHDNCL2ADNLC2AROBLD1HSPC162
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP97 (Homo sapiens)
Explore Q9NP97 
Go to UniProtKB:  Q9NP97
PHAROS:  Q9NP97
GTEx:  ENSG00000125971 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NP97
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain 1, cytoplasmicI [auth d],
N [auth i]
89Homo sapiensMutation(s): 0 
Gene Names: DYNLL1DLC1DNCL1DNCLC1HDLC1
UniProt & NIH Common Fund Data Resources
Find proteins for P63167 (Homo sapiens)
Explore P63167 
Go to UniProtKB:  P63167
PHAROS:  P63167
GTEx:  ENSG00000088986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63167
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain Tctex-type 1O [auth k],
P [auth v]
113Homo sapiensMutation(s): 0 
Gene Names: DYNLT1TCTEL1TCTEX-1TCTEX1
UniProt & NIH Common Fund Data Resources
Find proteins for P63172 (Homo sapiens)
Explore P63172 
Go to UniProtKB:  P63172
PHAROS:  P63172
GTEx:  ENSG00000146425 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63172
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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