4H25

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.0 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.USA 109: 18517-18522

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

  • 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 mole ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A, D
180Homo sapiensGene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens)
Go to Gene View: HLA-DRA
Go to UniProtKB:  P01903
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC class II antigen
B, E
188Homo sapiensGene Names: HLA-DRB3
Find proteins for B8YAC7 (Homo sapiens)
Go to Gene View: HLA-DRB3
Go to UniProtKB:  B8YAC7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
peptide
C, F
22N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download SDF File 
Download CCD File 
A, B, E
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 154.520α = 90.00
b = 97.180β = 105.36
c = 67.100γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
CNSrefinement
HKL-2000data reduction
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release