5DMK

Crystal Structure of IAg7 in complex with RLGL-WE14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

N-terminal additions to the WE14 peptide of chromogranin A create strong autoantigen agonists in type 1 diabetes.

Jin, N.Wang, Y.Crawford, F.White, J.Marrack, P.Dai, S.Kappler, J.W.

(2015) Proc Natl Acad Sci U S A 112: 13318-13323

  • DOI: https://doi.org/10.1073/pnas.1517862112
  • Primary Citation of Related Structures:  
    5DMK

  • PubMed Abstract: 

    Chromogranin A (ChgA) is an autoantigen for CD4(+) T cells in the nonobese diabetic (NOD) mouse model of type 1 diabetes (T1D). The natural ChgA-processed peptide, WE14, is a weak agonist for the prototypical T cell, BDC-2.5, and other ChgA-specific T-cell clones. Mimotope peptides with much higher activity share a C-terminal motif, WXRM(D/E), that is predicted to lie in the p5 to p9 position in the mouse MHC class II, IA(g7) binding groove. This motif is also present in WE14 (WSRMD), but at its N terminus. Therefore, to place the WE14 motif into the same position as seen in the mimotopes, we added the amino acids RLGL to its N terminus. Like the other mimotopes, RLGL-WE14, is much more potent than WE14 in T-cell stimulation and activates a diverse population of CD4(+) T cells, which also respond to WE14 as well as islets from WT, but not ChgA(-/-) mice. The crystal structure of the IA(g7)-RLGL-WE14 complex confirmed the predicted placement of the peptide within the IA(g7) groove. Fluorescent IA(g7)-RLGL-WE14 tetramers bind to ChgA-specific T-cell clones and easily detect ChgA-specific T cells in the pancreas and pancreatic lymph nodes of NOD mice. The prediction that many different N-terminal amino acid extensions to the WXRM(D/E) motif are sufficient to greatly improve T-cell stimulation leads us to propose that such a posttranslational modification may occur uniquely in the pancreas or pancreatic lymph nodes, perhaps via the mechanism of transpeptidation. This modification could account for the escape of these T cells from thymic negative selection.


  • Organizational Affiliation

    Howard Hughes Medical Institute, Denver, CO 80206; Department of Biomedical Research, National Jewish Health, Denver, CO 80206; Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO 80045;


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H-2 class II histocompatibility antigen, A-D alpha chain
A, C, E, G
173Mus musculusMutation(s): 0 
Gene Names: I-Ag7
UniProt
Find proteins for P04228 (Mus musculus)
Explore P04228 
Go to UniProtKB:  P04228
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04228
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein
B, D, F, H
212Mus musculusMutation(s): 0 
Gene Names: H2-Ab1
UniProt
Find proteins for P26339 (Mus musculus)
Explore P26339 
Go to UniProtKB:  P26339
Find proteins for Q31135 (Mus musculus)
Explore Q31135 
Go to UniProtKB:  Q31135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ31135P26339
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.765α = 90
b = 161.765β = 90
c = 204.162γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-11
    Changes: Database references
  • Version 1.2: 2016-04-06
    Changes: Source and taxonomy
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Structure summary