6VIH

The ligand-free structure of mouse RABL3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function.

Zhong, X.Su, L.Yang, Y.Nair-Gill, E.Tang, M.Anderton, P.Li, X.Wang, J.Zhan, X.Tomchick, D.R.Brautigam, C.A.Moresco, E.M.Y.Choi, J.H.Beutler, B.

(2020) Proc Natl Acad Sci U S A 117: 8563-8572

  • DOI: https://doi.org/10.1073/pnas.2000703117
  • Primary Citation of Related Structures:  
    6VIH, 6VII, 6VIJ, 6VIK

  • PubMed Abstract: 

    The small GTPase RABL3 is an oncogene of unknown physiological function. Homozygous knockout alleles of mouse Rabl3 were embryonic lethal, but a viable hypomorphic allele ( xiamen [ xm ]) causing in-frame deletion of four amino acids from the interswitch region resulted in profound defects in lymphopoiesis. Impaired lymphoid progenitor development led to deficiencies of B cells, T cells, and natural killer (NK) cells in Rabl3 xm/xm mice. T cells and NK cells exhibited impaired cytolytic activity, and mice infected with mouse cytomegalovirus (MCMV) displayed elevated titers in the spleen. Myeloid cells were normal in number and function. Biophysical and crystallographic studies demonstrated that RABL3 formed a homodimer in solution via interactions between the effector binding surfaces on each subunit; monomers adopted a typical small G protein fold. RABL3 xm displayed a large compensatory alteration in switch I, which adopted a β-strand configuration normally provided by the deleted interswitch residues, thereby permitting homodimer formation. Dysregulated effector binding due to conformational changes in the switch I-interswitch-switch II module likely underlies the xm phenotype. One such effector may be GPR89, putatively an ion channel or G protein-coupled receptor (GPCR). RABL3, but not RABL3 xm , strongly associated with and stabilized GPR89, and an N -ethyl- N -nitrosourea (ENU)-induced mutation ( explorer ) in Gpr89 phenocopied Rabl3 xm .


  • Organizational Affiliation

    Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390-8505.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rab-like protein 3A [auth B],
B [auth A]
245Mus musculusMutation(s): 0 
Gene Names: Rabl3
UniProt
Find proteins for Q9D4V7 (Mus musculus)
Explore Q9D4V7 
Go to UniProtKB:  Q9D4V7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9D4V7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.998α = 90
b = 79.2β = 90
c = 111.473γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

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)--

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Refinement description