6MP0

Crystal structures of the murine class I major histocompatibility complex H-2Db in complex with the TRP1-M9 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Altered Binding of Tumor Antigenic Peptides to MHC Class I Affects CD8+T Cell-Effector Responses.

Clancy-Thompson, E.Devlin, C.A.Tyler, P.M.Servos, M.M.Ali, L.R.Ventre, K.S.Bhuiyan, M.A.Bruck, P.T.Birnbaum, M.E.Dougan, S.K.

(2018) Cancer Immunol Res 6: 1524-1536

  • DOI: 10.1158/2326-6066.CIR-18-0348
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • T-cell priming occurs when a naïve T cell recognizes cognate peptide-MHC complexes on an activated antigen-presenting cell. The circumstances of this initial priming have ramifications on the fate of the newly primed T cell. Newly primed CD8 <sup>+ < ...

    T-cell priming occurs when a naïve T cell recognizes cognate peptide-MHC complexes on an activated antigen-presenting cell. The circumstances of this initial priming have ramifications on the fate of the newly primed T cell. Newly primed CD8 + T cells can embark onto different trajectories, with some becoming short-lived effector cells and others adopting a tissue resident or memory cell fate. To determine whether T-cell priming influences the quality of the effector T-cell response to tumors, we used transnuclear CD8 + T cells that recognize the melanoma antigen TRP1 using TRP1 high or TRP1 low TCRs that differ in both affinity and fine specificity. From a series of altered peptide ligands, we identified a point mutation (K8) in a nonanchor residue that, when analyzed crystallographically and biophysically, destabilized the peptide interaction with the MHC binding groove. In vitro , the K8 peptide induced robust proliferation of both TRP1 high and TRP1 low CD8 + T cells but did not induce expression of PD-1. Cytokine production from K8-stimulated TRP1 cells was minimal, whereas cytotoxicity was increased. Upon transfer into B16 tumor-bearing mice, the reference peptide (TRP1-M9)- and K8-stimulated TRP1 cells were equally effective at controlling tumor growth but accomplished this through different mechanisms. TRP1-M9-stimulated cells produced more IFNγ, whereas K8-stimulated cells accumulated to higher numbers and were more cytotoxic. We, therefore, conclude that TCR recognition of weakly binding peptides during priming can skew the effector function of tumor-specific CD8 + T cells.


    Organizational Affiliation

    Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts.,Department of Biological Engineering, Massachusetts Institute of Technology, Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts.,Department of Biological Engineering, Massachusetts Institute of Technology, Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts. Stephanie_dougan@dfci.harvard.edu mbirnb@mit.edu.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts. Stephanie_dougan@dfci.harvard.edu mbirnb@mit.edu.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRP1-M9 peptide, Beta-2-microglobulin,H-2 class I histocompatibility antigen, D-B alpha chain, chimeric construct
A
447Mus musculusMutation(s): 2 
Gene Names: H2-D1, Tyrp1 (Tyrp-1), B2m
EC: 1.14.18.-
Find proteins for P01899 (Mus musculus)
Go to UniProtKB:  P01899
Find proteins for P07147 (Mus musculus)
Go to UniProtKB:  P07147
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.061α = 90.00
b = 98.436β = 90.00
c = 121.772γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesP30-CA14051
National Institutes of Health/National Cancer InstituteUnited StatesT32CA207021

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-28
    Type: Data collection, Database references
  • Version 1.2: 2018-12-12
    Type: Data collection, Database references