9LX0 | pdb_00009lx0

DOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.98 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

Conformational alteration of DOCK5•ELMO1 signalosome on lipid membrane.

Shinoda, T.Katsura, K.Ishizuka-Katsura, Y.Hanada, K.Yonemochi, M.Miyamoto, Y.Kukimoto-Niino, M.Yamauchi, J.Shirouzu, M.

(2025) Commun Biol 8: 1523-1523

  • DOI: https://doi.org/10.1038/s42003-025-09113-5
  • Primary Citation of Related Structures:  
    9LX0, 9LXH

  • PubMed Abstract: 

    The DOCK protein family activates Rho small GTPases through guanine nucleotide exchange factor (GEF) activity. DOCK is thought to exert its GEF activity at the plasma membrane. However, the mechanism by which DOCK activity on the plasma membrane is regulated remains unclear. Herein, we present a new conformation in which DOCK5, ELMO1, RhoG, and Rac1 are aligned on a plane and symmetrically flattened, as revealed by cryo-EM using a lipid membrane-coated grid. The major conformational change leading to this structure results from rotation of each DOCK5•ELMO1 hinge site through interactions with the membrane. Biochemical and cellular experiments indicate that conformational changes driven by acidic lipids are important for regulating the GEF activity of the DOCK5•ELMO1 complex on the plasma membrane and are essential for its downstream signalling. This approach also enables the analysis of large lipid-associated complexes, such as signalosomes, and will aid studies of membrane-dependent signalling assemblies.


  • Organizational Affiliation
    • Laboratory for Functional and Structural Biology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Engulfment and cell motility protein 1
A, E
733Homo sapiensMutation(s): 0 
Gene Names: ELMO1KIAA0281
UniProt & NIH Common Fund Data Resources
Find proteins for Q92556 (Homo sapiens)
Explore Q92556 
Go to UniProtKB:  Q92556
PHAROS:  Q92556
GTEx:  ENSG00000155849 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92556
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dedicator of cytokinesis protein 5
B, F
1,876Homo sapiensMutation(s): 1 
Gene Names: DOCK5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7D0 (Homo sapiens)
Explore Q9H7D0 
Go to UniProtKB:  Q9H7D0
PHAROS:  Q9H7D0
GTEx:  ENSG00000147459 
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UniProt GroupQ9H7D0
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Rho-related GTP-binding protein RhoG
C, G
214Homo sapiensMutation(s): 1 
Gene Names: RHOGARHG
UniProt & NIH Common Fund Data Resources
Find proteins for P84095 (Homo sapiens)
Explore P84095 
Go to UniProtKB:  P84095
PHAROS:  P84095
GTEx:  ENSG00000177105 
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UniProt GroupP84095
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related C3 botulinum toxin substrate 1
D, H
206Homo sapiensMutation(s): 1 
Gene Names: RAC1TC25MIG5
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63000 (Homo sapiens)
Explore P63000 
Go to UniProtKB:  P63000
PHAROS:  P63000
GTEx:  ENSG00000136238 
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UniProt GroupP63000
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanCREST JPMJCR22E3

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Data collection, Database references