4H1L

TCR interaction with peptide mimics of nickel offers structural insights in nickel contact allergy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.264 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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 DR52c containing an unknown self-peptide ...

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chainA, D178Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
Find proteins for P01903 (Homo sapiens)
Explore P01903 
Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS:  P01903
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class II antigenB, E187Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB3
Find proteins for P79483 (Homo sapiens)
Explore P79483 
Go to UniProtKB:  P79483
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
mimotope peptideC, F13Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Ani2.3 TCR A chainG, I113Escherichia coliMutation(s): 0 
Find proteins for L7MTK9 (Escherichia coli)
Explore L7MTK9 
Go to UniProtKB:  L7MTK9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ani2.3 TCR B chainH, J111Escherichia coliMutation(s): 0 
Find proteins for L7MTL0 (Escherichia coli)
Explore L7MTL0 
Go to UniProtKB:  L7MTL0
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.264 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.722α = 90
b = 186.722β = 90
c = 166.702γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references