4P5M | pdb_00004p5m

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.204 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.2 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: https://doi.org/10.1016/j.cell.2014.04.048
  • Primary Citation Related Structures: 
    4P4K, 4P4R, 4P57, 4P5K, 4P5M

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 186.42 kDa 
  • Atom Count: 14,385 
  • Modeled Residue Count: 1,499 
  • Deposited Residue Count: 1,580 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DP alpha 1 chain
A, C, E, G
183Homo sapiensMutation(s): 0 
Gene Names: HLA-DPA1HLA-DP1AHLASB
UniProt & NIH Common Fund Data Resources
Find proteins for P20036 (Homo sapiens)
Explore P20036 
Go to UniProtKB:  P20036
PHAROS:  P20036
GTEx:  ENSG00000231389 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20036
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P20036-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
peptide,HLA class II histocompatibility antigen, DP beta 1 chain
B, D, F, H
212Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P04440 (Homo sapiens)
Explore P04440 
Go to UniProtKB:  P04440
PHAROS:  P04440
GTEx:  ENSG00000223865 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04440
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P04440-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, K, N
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
J
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G57331KL
GlyCosmos: G57331KL
GlyGen: G57331KL
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
L
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G26744ZJ
GlyCosmos: G26744ZJ
GlyGen: G26744ZJ
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-D-mannopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
M
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G59760RN
GlyCosmos: G59760RN
GlyGen: G59760RN
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
O
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G29706YY
GlyCosmos: G29706YY
GlyGen: G29706YY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.204 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.631α = 90
b = 130.468β = 107.16
c = 107.994γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Derived calculations
  • Version 1.2: 2015-10-14
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 2.2: 2024-10-23
    Changes: Structure summary