4P5M

Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic Hypersensitivity and Autoimmunity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of chronic beryllium disease: linking allergic hypersensitivity and autoimmunity.

Clayton, G.M.Wang, Y.Crawford, F.Novikov, A.Wimberly, B.T.Kieft, J.S.Falta, M.T.Bowerman, N.A.Marrack, P.Fontenot, A.P.Dai, S.Kappler, J.W.

(2014) Cell 158: 132-142

  • DOI: 10.1016/j.cell.2014.04.048
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • T-cell-mediated hypersensitivity to metal cations is common in humans. How the T cell antigen receptor (TCR) recognizes these cations bound to a major histocompatibility complex (MHC) protein and self-peptide is unknown. Individuals carrying the MHCI ...

    T-cell-mediated hypersensitivity to metal cations is common in humans. How the T cell antigen receptor (TCR) recognizes these cations bound to a major histocompatibility complex (MHC) protein and self-peptide is unknown. Individuals carrying the MHCII allele, HLA-DP2, are at risk for chronic beryllium disease (CBD), a debilitating inflammatory lung condition caused by the reaction of CD4 T cells to inhaled beryllium. Here, we show that the T cell ligand is created when a Be(2+) cation becomes buried in an HLA-DP2/peptide complex, where it is coordinated by both MHC and peptide acidic amino acids. Surprisingly, the TCR does not interact with the Be(2+) itself, but rather with surface changes induced by the firmly bound Be(2+) and an accompanying Na(+) cation. Thus, CBD, by creating a new antigen by indirectly modifying the structure of preexisting self MHC-peptide complex, lies on the border between allergic hypersensitivity and autoimmunity.


    Organizational Affiliation

    Howard Hughes Medical Institute, National Jewish Health, Denver, CO 80206, USA; Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA; Department of Immunology and Microbiology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DP alpha 1 chain
A, C, E, G
183Homo sapiensMutation(s): 0 
Gene Names: HLA-DPA1 (HLA-DP1A, HLASB)
Find proteins for P20036 (Homo sapiens)
Go to Gene View: HLA-DPA1
Go to UniProtKB:  P20036
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide,HLA class II histocompatibility antigen, DP beta 1 chain
B, D, F, H
212Homo sapiensMutation(s): 0 
Gene Names: HLA-DPB1 (HLA-DP1B)
Find proteins for P04440 (Homo sapiens)
Go to Gene View: HLA-DPB1
Go to UniProtKB:  P04440
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
F, H
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.631α = 90.00
b = 130.468β = 107.16
c = 107.994γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Derived calculations
  • Version 1.2: 2015-10-14
    Type: Data collection