8JHK

Cryo-EM structure of the DOCK5/ELMO1 complex, focused on one protomer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

RhoG facilitates a conformational transition in the guanine nucleotide exchange factor complex DOCK5/ELMO1 to an open state.

Kukimoto-Niino, M.Katsura, K.Ishizuka-Katsura, Y.Mishima-Tsumagari, C.Yonemochi, M.Inoue, M.Nakagawa, R.Kaushik, R.Zhang, K.Y.J.Shirouzu, M.

(2024) J Biol Chem 300: 107459-107459

  • DOI: https://doi.org/10.1016/j.jbc.2024.107459
  • Primary Citation of Related Structures:  
    8JHK, 8XM7, 8ZJ2, 8ZJI, 8ZJJ, 8ZJK, 8ZJL, 8ZJM

  • PubMed Abstract: 

    The dedicator of cytokinesis (DOCK)/engulfment and cell motility (ELMO) complex serves as a guanine nucleotide exchange factor (GEF) for the GTPase Rac. RhoG, another GTPase, activates the ELMO-DOCK-Rac pathway during engulfment and migration. Recent cryo-EM structures of the DOCK2/ELMO1 and DOCK2/ELMO1/Rac1 complexes have identified closed and open conformations that are key to understanding the autoinhibition mechanism. Nevertheless, the structural details of RhoG-mediated activation of the DOCK/ELMO complex remain elusive. Herein, we present cryo-EM structures of DOCK5/ELMO1 alone and in complex with RhoG and Rac1. The DOCK5/ELMO1 structure exhibits a closed conformation similar to that of DOCK2/ELMO1, suggesting a shared regulatory mechanism of the autoinhibitory state across DOCK-A/B subfamilies (DOCK1-5). Conversely, the RhoG/DOCK5/ELMO1/Rac1 complex adopts an open conformation that differs from that of the DOCK2/ELMO1/Rac1 complex, with RhoG binding to both ELMO1 and DOCK5. The alignment of the DOCK5 PIP3 binding site with the RhoG C-terminal lipidation site suggests simultaneous binding of RhoG and DOCK5/ELMO1 to the plasma membrane. Structural comparison of the apo and RhoG-bound states revealed that RhoG facilitates a closed-to-open state conformational change of DOCK5/ELMO1. Biochemical and surface plasmon resonance (SPR) assays confirm that RhoG enhances the Rac GEF activity of DOCK5/ELMO1 and increases its binding affinity for Rac1. Further analysis of structural variability underscored the conformational flexibility of the DOCK5/ELMO1/Rac1 complex core, potentially facilitating the proximity of the DOCK5 GEF domain to the plasma membrane. These findings elucidate the structural mechanism underlying the RhoG-induced allosteric activation and membrane binding of the DOCK/ELMO complex.


  • Organizational Affiliation

    RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. Electronic address: kukimoto@riken.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Engulfment and cell motility protein 1733Homo 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dedicator of cytokinesis protein 5B,
C [auth E]
1,648Homo 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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H7D0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanKAKENHI JP19K06575
Japan Society for the Promotion of Science (JSPS)JapanKAKENHI JP22H05551
Japan Science and TechnologyJapanCREST JPMJCR22E3

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2024-07-17
    Changes: Data collection, Database references