4NO0

Crystal structure of non-phosphorylated form of RQA_V phosphopeptide bound to HLA-A2 in complex with LILRB1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.271 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status.

Mohammed, F.Stones, D.H.Zarling, A.L.Willcox, C.R.Shabanowitz, J.Cummings, K.L.Hunt, D.F.Cobbold, M.Engelhard, V.H.Willcox, B.E.

(2017) Oncotarget 8: 54160-54172

  • DOI: https://doi.org/10.18632/oncotarget.16952
  • Primary Citation of Related Structures:  
    4NNX, 4NNY, 4NO0, 4NO2, 4NO3, 4NO5

  • PubMed Abstract: 

    Dysregulated post-translational modification provides a source of altered self-antigens that can stimulate immune responses in autoimmunity, inflammation, and cancer. In recent years, phosphorylated peptides have emerged as a group of tumour-associated antigens presented by MHC molecules and recognised by T cells, and represent promising candidates for cancer immunotherapy. However, the impact of phosphorylation on the antigenic identity of phosphopeptide epitopes is unclear. Here we examined this by determining structures of MHC-bound phosphopeptides bearing canonical position 4-phosphorylations in the presence and absence of their phosphate moiety, and examining phosphopeptide recognition by the T cell receptor (TCR). Strikingly, two peptides exhibited major conformational changes upon phosphorylation, involving a similar molecular mechanism, which focussed changes on the central peptide region most critical for T cell recognition. In contrast, a third epitope displayed little conformational alteration upon phosphorylation. In addition, binding studies demonstrated TCR interaction with an MHC-bound phosphopeptide was both epitope-specific and absolutely dependent upon phosphorylation status. These results highlight the critical influence of phosphorylation on the antigenic identity of naturally processed class I MHC epitopes. In doing so they provide a molecular framework for understanding phosphopeptide-specific immune responses, and have implications for the development of phosphopeptide antigen-specific cancer immunotherapy approaches.


  • Organizational Affiliation

    Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chain276Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
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Find proteins for P04439 (Homo sapiens)
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Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
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UniProt GroupP04439
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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Find proteins for P61769 (Homo sapiens)
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Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Lymphocyte-specific protein 112Homo sapiensMutation(s): 0 
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Find proteins for P33241 (Homo sapiens)
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PHAROS:  P33241
GTEx:  ENSG00000130592 
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UniProt GroupP33241
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Leukocyte immunoglobulin-like receptor subfamily B member 1195Homo sapiensMutation(s): 0 
Gene Names: ILT2LILRB1LIR1MIR7
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Find proteins for Q8NHL6 (Homo sapiens)
Explore Q8NHL6 
Go to UniProtKB:  Q8NHL6
PHAROS:  Q8NHL6
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UniProt GroupQ8NHL6
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.271 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.3α = 90
b = 117.3β = 90
c = 96.1γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Database references
  • Version 1.2: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.3: 2023-09-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description