2BNQ

Structural and kinetic basis for heightened immunogenicity of T cell vaccines


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and Kinetic Basis for Heightened Immunogenicity of T Cell Vaccines

Chen, J.-L.Stewart-Jones, G.Bossi, G.Lissin, N.M.Wooldridge, L.Choi, E.M.L.Held, G.Dunbar, P.R.Esnouf, R.M.Sami, M.Boultier, J.M.Rizkallah, P.Renner, C.Sewell, A.Van Der Merwe, P.A.Jackobsen, B.K.Griffiths, G.Jones, E.Y.Cerundolo, V.

(2005) J Exp Med 201: 1243

  • DOI: 10.1084/jem.20042323
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Analogue peptides with enhanced binding affinity to major histocompatibility class (MHC) I molecules are currently being used in cancer patients to elicit stronger T cell responses. However, it remains unclear as to how alterations of anchor residues ...

    Analogue peptides with enhanced binding affinity to major histocompatibility class (MHC) I molecules are currently being used in cancer patients to elicit stronger T cell responses. However, it remains unclear as to how alterations of anchor residues may affect T cell receptor (TCR) recognition. We correlate functional, thermodynamic, and structural parameters of TCR-peptide-MHC binding and demonstrate the effect of anchor residue modifications of the human histocompatibility leukocyte antigens (HLA)-A2 tumor epitope NY-ESO-1(157-165)-SLLMWITQC on TCR recognition. The crystal structure of the wild-type peptide complexed with a specific TCR shows that TCR binding centers on two prominent, sequential, peptide sidechains, methionine-tryptophan. Cysteine-to-valine substitution at peptide position 9, while optimizing peptide binding to the MHC, repositions the peptide main chain and generates subtly enhanced interactions between the analogue peptide and the TCR. Binding analyses confirm tighter binding of the analogue peptide to HLA-A2 and improved soluble TCR binding. Recognition of analogue peptide stimulates faster polarization of lytic granules to the immunological synapse, reduces dependence on CD8 binding, and induces greater numbers of cross-reactive cytotoxic T lymphocyte to SLLMWITQC. These results provide important insights into heightened immunogenicity of analogue peptides and highlight the importance of incorporating structural data into the process of rational optimization of superagonist peptides for clinical trials.


    Related Citations: 
    • Identification of NY-Eso-1 Peptide Analogues Capable of Improved Stimulation of Tumor-Reactive Ctl
      Chen, J.-L., Dunbar, P.R., Gileadi, U., Jager, E., Gnjatic, S., Nagata, Y., Stockert, E., Panicali, D.L., Chen, Y.-T., Knuth, A., Old, L.J., Cerundolo, V.
      (2000) J Immunol 165: 948

    Organizational Affiliation

    Tumour Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA CLASS I HISTOCOMPATIBILITY ANTIGENA276Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
Find proteins for P04439 (Homo sapiens)
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PHAROS  P04439
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SYNTHETIC PEPTIDEC9Homo sapiensMutation(s): 0 
Gene Names: CTAG1ACTAGCTAG1ESO1LAGE2LAGE2ACTAG1BLAGE2B
Find proteins for P78358 (Homo sapiens)
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PHAROS  P78358
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T-CELL RECEPTOR ALPHA CHAIN V REGIOND203Homo sapiensMutation(s): 0 
Gene Names: TRACTCRATRAV21
Find proteins for P01848 (Homo sapiens)
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PHAROS  P01848
Find proteins for A0A0B4J279 (Homo sapiens)
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PHAROS  A0A0B4J279
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
T-CELL RECEPTOR BETA CHAIN C REGIONE241Homo sapiensMutation(s): 0 
Gene Names: TRBC1TRBV6-5
Find proteins for A0A0K0K1A5 (Homo sapiens)
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PHAROS  A0A0K0K1A5
Find proteins for P01850 (Homo sapiens)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BETA-2-MICROGLOBULINB100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
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PHAROS  P61769
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.563α = 90
b = 62.49β = 105.34
c = 116.955γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

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Entry History 

Revision History 

  • Version 1.0: 2005-05-23
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance