8YO0

Crystal Structure of Human Rab23 Y79del in Complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural basis for Rab23 activation and a loss-of-function mutation in Carpenter Syndrome.

Chau, Y.Y.Liang, H.Tung, W.L.Hor, C.H.H.Aik, W.S.

(2024) J Biol Chem : 108036-108036

  • DOI: https://doi.org/10.1016/j.jbc.2024.108036
  • Primary Citation of Related Structures:  
    8YIM, 8YL3, 8YNR, 8YO0, 8YP0

  • PubMed Abstract: 

    Rab23 is a member of the Rab family of small GTPases. It plays crucial roles in Hedgehog signaling, ciliary transport, and embryonic development. As a small GTPase, Rab23 cycles between the GDP-bound inactivated state and the GTP-bound activated state. Mutations in Rab23 is directly implicated in Carpenter Syndrome, a development disorder characterized by deformed skulls, abnormal fingers or toes, and intellectual disabilities. Several clinical point mutations, e.g. M12K, C85R and Y79del, have been found to occur within the GTPase domain. However, the mechanisms of activation of Rab23 and pathogenesis of its clinical mutants are still unclear with limited structural information. So far, there are only two reported crystal structures of mouse Rab23 in complex with GDP. Here, we determined high-resolution crystal structures of human Rab23 and the human Rab23 Y79del clinical mutant, in complex with GDP and GMPPNP, a non-hydrolysable GTP analogue, respectively. Supported by in vitro biochemical and functional analyses, we demonstrated that the Y79 deletion mutant exhibited structural distortions in the Switch II region relative to that of the wild-type. The structural changes potentially disrupted the binding of Rab23 Y79del to its interacting partners, thus leading to a loss-of-function and the development of Carpenter Syndrome.


  • Organizational Affiliation

    Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-23166Homo sapiensMutation(s): 0 
Gene Names: RAB23HSPC137
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULC3 (Homo sapiens)
Explore Q9ULC3 
Go to UniProtKB:  Q9ULC3
PHAROS:  Q9ULC3
GTEx:  ENSG00000112210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ULC3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.787α = 90
b = 51.606β = 90
c = 74.597γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata scaling
CrysalisProdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateHong KongHKBU Faculty of Science Seed Money

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2024-12-18
    Changes: Database references