4P4K

Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between allergic hypersensitivity and auto immunity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

    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; Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA.,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.,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; Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, 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.,Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA.,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; Program in Structural Biology and Biochemistry, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA. Electronic address: kapplerj@njhealth.org.,Department of Biochemistry and Molecular Genetics, Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; Program in Structural Biology and Biochemistry, University of Colorado Denver School of Medicine, Aurora, CO 80045, 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. Electronic address: dais@njhealth.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DP alpha 1 chain
A, E
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
mim2 peptide,HLA class II histocompatibility antigen, DP beta 1 chain
B, F
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
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
hTCRav22 alpha chain
C, G
209Homo sapiensMutation(s): 0 
Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
hTCRav22 beta chain
D, H
242Homo sapiensMutation(s): 0 
Gene Names: TRBC2 (TCRBC2)
Find proteins for A0A5B9 (Homo sapiens)
Go to UniProtKB:  A0A5B9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
B, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
0BE
Query on 0BE

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Download CCD File 
B, F
BERYLLIUM
Be
PWOSZCQLSAMRQW-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 79.400α = 90.00
b = 137.240β = 90.00
c = 213.130γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2015-01-07
    Type: Database references