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: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1158/2326-6066.CIR-18-0348
  • Primary Citation of Related Structures:  
    6MP0, 6MP1

  • 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 + 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 Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRP1-M9 peptide, Beta-2-microglobulin,H-2 class I histocompatibility antigen, D-B alpha chain, chimeric construct447Mus musculusMutation(s): 2 
Gene Names: Tyrp1Tyrp-1B2mH2-D1
EC: 1.14.18
UniProt & NIH Common Fund Data Resources
Find proteins for P01899 (Mus musculus)
Explore P01899 
Go to UniProtKB:  P01899
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
Find proteins for P07147 (Mus musculus)
Explore P07147 
Go to UniProtKB:  P07147
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP01899P01887P07147
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.061α = 90
b = 98.436β = 90
c = 121.772γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30-CA14051
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesT32CA207021

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-12
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary