3TIE | pdb_00003tie

Crystal structure of the vaccinia derived peptide A11R in complex with the murine MHC CLASS I H-2 KB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.219 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3TIE

This is version 1.3 of the entry. See complete history

Literature

Disparate epitopes mediating protective heterologous immunity to unrelated viruses share peptide-MHC structural features recognized by cross-reactive T cells.

Shen, Z.T.Nguyen, T.T.Daniels, K.A.Welsh, R.M.Stern, L.J.

(2013) J Immunol 191: 5139-5152

  • DOI: https://doi.org/10.4049/jimmunol.1300852
  • Primary Citation Related Structures: 
    3TID, 3TIE

  • PubMed Abstract: 

    Closely related peptide epitopes can be recognized by the same T cells and contribute to the immune response against pathogens encoding those epitopes, but sometimes cross-reactive epitopes share little homology. The degree of structural homology required for such disparate ligands to be recognized by cross-reactive TCRs remains unclear. In this study, we examined the mechanistic basis for cross-reactive T cell responses between epitopes from unrelated and pathogenic viruses, lymphocytic choriomeningitis virus (LCMV) and vaccinia virus. Our results show that the LCMV cross-reactive T cell response toward vaccinia virus is dominated by a shared asparagine residue, together with other shared structural elements conserved in the crystal structures of K(b)-VV-A11R and K(b)-LCMV-gp34. Based on analysis of the crystal structures and the specificity determinants for the cross-reactive T cell response, we were able to manipulate the degree of cross-reactivity of the T cell response, and to predict and generate a LCMV cross-reactive response toward a variant of a null OVA-derived peptide. These results indicate that protective heterologous immune responses can occur for disparate epitopes from unrelated viruses.


  • Organizational Affiliation
    • Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655.

Macromolecule Content 

  • Total Structure Weight: 91.13 kDa 
  • Atom Count: 6,738 
  • Modeled Residue Count: 768 
  • Deposited Residue Count: 782 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, K-B alpha chainA,
C [auth D]
284Mus musculusMutation(s): 0 
Gene Names: H2-K1H2-K
UniProt
Find proteins for P01901 (Mus musculus)
Explore P01901 
Go to UniProtKB:  P01901
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01901
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulinB,
D [auth E]
99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Vaccinia derived octamer peptideE [auth C],
F
8Orthopoxvirus vacciniaMutation(s): 0 
UniProt
Find proteins for Q49PI7 (Vaccinia virus (strain LC16m0))
Explore Q49PI7 
Go to UniProtKB:  Q49PI7
Entity Groups
UniProt GroupQ49PI7
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.219 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.264α = 90
b = 84.71β = 98.12
c = 87.895γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
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: 2012-08-22
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-11-27
    Changes: Structure summary