4H25

TCR interaction with peptide mimics of nickel offers structure insights to nickel contact allergy

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.220 

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Literature

T-cell receptor (TCR) interaction with peptides that mimic nickel offers insight into nickel contact allergy.

Yin, L., Crawford, F., Marrack, P., Kappler, J.W., Dai, S.

(2012) Proc Natl Acad Sci U S A 109: 18517-18522

  • DOI: 10.1073/pnas.1215928109
  • Primary Citation of Related Structures:  
    4H26, 4H25, 4H1L

  • PubMed Abstract: 

    • T cell-mediated allergy to Ni(++) is one of the most common forms of allergic contact dermatitis, but how the T-cell receptor (TCR) recognizes Ni(++) is unknown. We studied a TCR from an allergic patient that recognizes Ni(++) bound to the MHCII molecule ...

    T cell-mediated allergy to Ni(++) is one of the most common forms of allergic contact dermatitis, but how the T-cell receptor (TCR) recognizes Ni(++) is unknown. We studied a TCR from an allergic patient that recognizes Ni(++) bound to the MHCII molecule DR52c containing an unknown self-peptide. We identified mimotope peptides that can replace both the self-peptide and Ni(++) in this ligand. They share a p7 lysine whose εNH(2) group is surface-exposed when bound to DR52c. Whereas the TCR uses germ-line complementary-determining region (CDR)1/2 amino acids to dock in the conventional diagonal mode on the mimotope-DR52c complex, the interface is dominated by the TCR Vβ CDR3 interaction with the p7 lysine. Mutations in the TCR CDR loops have similar effects on the T-cell response to either the mimotope or Ni(++) ligand. We suggest that the mimotope p7 lysine mimics Ni(++) in the natural TCR ligand and that MHCII β-chain flexibility in the area around the peptide p7 position forms a common site for cation binding in metal allergies.

    Organizational Affiliation: 

    Howard Hughes Medical Institute, National Jewish Health, Denver, CO 80206, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain A, D180Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA, HLA-DRA1
Find proteins for P01903 (Homo sapiens)
Explore P01903 
Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS:  P01903
GTEx:  ENSG00000204287
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class II antigen B, E188Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB3
Find proteins for B8YAC7 (Homo sapiens)
Explore B8YAC7 
Go to UniProtKB:  B8YAC7
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
peptide C, F22N/AMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, J, K, L
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.52α = 90
b = 97.18β = 105.36
c = 67.1γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary