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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 112: 13318-13323

  • DOI: 10.1073/pnas.1517862112

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class II histocompatibility antigen, A-D alpha chain
A, C, E, G
173Mus musculusGene Names: H2-Aa
Find proteins for P04228 (Mus musculus)
Go to UniProtKB:  P04228
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein
B, D, F, H
212Mus musculusGene Names: Chga, H2-Ab1
Find proteins for P26339 (Mus musculus)
Go to UniProtKB:  P26339
Find proteins for Q31135 (Mus musculus)
Go to UniProtKB:  Q31135
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download SDF File 
Download CCD File 
B, F
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.211 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 161.765α = 90.00
b = 161.765β = 90.00
c = 204.162γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-11
    Type: Database references
  • Version 1.2: 2016-04-06
    Type: Source and taxonomy