8IJ9

Crystal structure of the ELKS1/Rab6B complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Literature

Structural basis of ELKS/Rab6B interaction and its role in vesicle capturing enhanced by liquid-liquid phase separation.

Jin, G.Lin, L.Li, K.Li, J.Yu, C.Wei, Z.

(2023) J Biol Chem 299: 104808-104808

  • DOI: https://doi.org/10.1016/j.jbc.2023.104808
  • Primary Citation of Related Structures:  
    8IJ9

  • PubMed Abstract: 

    ELKS proteins play a key role in organizing intracellular vesicle trafficking and targeting in both neurons and non-neuronal cells. While it is known that ELKS interacts with the vesicular traffic regulator, the Rab6 GTPase, the molecular basis governing ELKS-mediated trafficking of Rab6-coated vesicles, has remained unclear. In this study, we solved the Rab6B structure in complex with the Rab6-binding domain of ELKS1, revealing that a C-terminal segment of ELKS1 forms a helical hairpin to recognize Rab6B through a unique binding mode. We further showed that liquid-liquid phase separation (LLPS) of ELKS1 allows it to compete with other Rab6 effectors for binding to Rab6B and accumulate Rab6B-coated liposomes to the protein condensate formed by ELKS1. We also found that the ELKS1 condensate recruits Rab6B-coated vesicles to vesicle-releasing sites and promotes vesicle exocytosis. Together, our structural, biochemical, and cellular analyses suggest that ELKS1, via the LLPS-enhanced interaction with Rab6, captures Rab6-coated vesicles from the cargo transport machine for efficient vesicle release at exocytotic sites. These findings shed new light on the understanding of spatiotemporal regulation of vesicle trafficking through the interplay between membranous structures and membraneless condensates.


  • Organizational Affiliation

    Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-6B
A, B
173Mus musculusMutation(s): 1 
Gene Names: Rab6bD9Bwg0185e
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61294 (Mus musculus)
Explore P61294 
Go to UniProtKB:  P61294
IMPC:  MGI:107283
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61294
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ELKS/Rab6-interacting/CAST family member 1
C, D
78Rattus norvegicusMutation(s): 0 
Gene Names: Erc1Cast2ElksRab6ip2
UniProt
Find proteins for Q811U3 (Rattus norvegicus)
Explore Q811U3 
Go to UniProtKB:  Q811U3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ811U3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.193α = 90
b = 93.227β = 103.74
c = 53.077γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31971131
National Natural Science Foundation of China (NSFC)China32170697

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references