8CZ9

Crystal Structure of the E372K LNK SH2 Domain mutant in Complex with a JAK2 pY813 Phosphopeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Rare SH2B3 coding variants in lupus patients impair B cell tolerance and predispose to autoimmunity.

Zhang, Y.Morris, R.Brown, G.J.Lorenzo, A.M.D.Meng, X.Kershaw, N.J.Kiridena, P.Burgio, G.Gross, S.Cappello, J.Y.Shen, Q.Wang, H.Turnbull, C.Lea-Henry, T.Stanley, M.Yu, Z.Ballard, F.D.Chuah, A.Lee, J.C.Hatch, A.M.Enders, A.Masters, S.L.Headley, A.P.Trnka, P.Mallon, D.Fletcher, J.T.Walters, G.D.Sestan, M.Jelusic, M.Cook, M.C.Athanasopoulos, V.Fulcher, D.A.Babon, J.J.Vinuesa, C.G.Ellyard, J.I.

(2024) J Exp Med 221

  • DOI: https://doi.org/10.1084/jem.20221080
  • Primary Citation of Related Structures:  
    8CZ9

  • PubMed Abstract: 

    Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease with a clear genetic component. While most SLE patients carry rare gene variants in lupus risk genes, little is known about their contribution to disease pathogenesis. Amongst them, SH2B3-a negative regulator of cytokine and growth factor receptor signaling-harbors rare coding variants in over 5% of SLE patients. Here, we show that unlike the variant found exclusively in healthy controls, SH2B3 rare variants found in lupus patients are predominantly hypomorphic alleles, failing to suppress IFNGR signaling via JAK2-STAT1. The generation of two mouse lines carrying patients' variants revealed that SH2B3 is important in limiting the number of immature and transitional B cells. Furthermore, hypomorphic SH2B3 was shown to impair the negative selection of immature/transitional self-reactive B cells and accelerate autoimmunity in sensitized mice, at least in part due to increased IL-4R signaling and BAFF-R expression. This work identifies a previously unappreciated role for SH2B3 in human B cell tolerance and lupus risk.


  • Organizational Affiliation

    Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Acton, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SH2B adapter protein 3110Mus musculusMutation(s): 1 
Gene Names: Sh2b3Lnk
UniProt
Find proteins for O09039 (Mus musculus)
Explore O09039 
Go to UniProtKB:  O09039
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO09039
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
JAK2 pY813 phosphopeptideB [auth C]8Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O60674 (Homo sapiens)
Explore O60674 
Go to UniProtKB:  O60674
PHAROS:  O60674
GTEx:  ENSG00000096968 
Entity Groups  
UniProt GroupO60674
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
B [auth C]L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.829α = 90
b = 37.618β = 108.76
c = 50.497γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-15
    Changes: Data collection
  • Version 1.3: 2024-03-13
    Changes: Database references