7T5M

Structure of HLA-A*02:01-FLPTPEELGLLGPPRPQVLA complex

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-12-12 Released: 2022-12-14 
  • Deposition Author(s): Gras, S.
  • Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cutting Edge: Unconventional CD8 + T Cell Recognition of a Naturally Occurring HLA-A*02:01-Restricted 20mer Epitope.

Meeuwsen, M.H.Wouters, A.K.Hagedoorn, R.S.Kester, M.G.D.Remst, D.F.G.van der Steen, D.M.de Ru, A.van Veelen, P.A.Rossjohn, J.Gras, S.Falkenburg, J.H.F.Heemskerk, M.H.M.

(2022) J Immunol 208: 1851-1856

  • DOI: https://doi.org/10.4049/jimmunol.2101208
  • Primary Citation of Related Structures:  
    7T5M

  • PubMed Abstract: 

    Unconventional HLA class I-restricted CD8 + T cell epitopes, longer than 10 aa, have been implicated to play a role in human immunity against viruses and cancer. T cell recognition of long peptides, centrally bulging from the HLA cleft, has been described previously. Alternatively, long peptides can contain a linear HLA-bound core peptide, with a N- or C-terminal peptide "tail" extending from the HLA peptide binding groove. The role of such a peptide "tail" in CD8 + T cell recognition remains unclear. In this study, we identified a 20mer peptide (FLPTPEELGLLGPPRPQVLA [FLP]) derived from the IL-27R subunit α gene restricted to HLA-A*02:01, for which we solved the crystal structure and demonstrated a long C-terminal "tail" extension. FLP-specific T cell clones demonstrated various recognition modes, some T cells recognized the FLP core peptide, while for other T cells the peptide tail was essential for recognition. These results demonstrate a crucial role for a C-terminal peptide tail in immunogenicity.


  • Organizational Affiliation

    Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands; m.h.meeuwsen@lumc.nl m.h.m.heemskerk@lumc.nl.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen
A, C
278Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for Q861F7 (Homo sapiens)
Explore Q861F7 
Go to UniProtKB:  Q861F7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ861F7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, D
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
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-27 receptor subunit alpha
E, F
20Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6UWB1 (Homo sapiens)
Explore Q6UWB1 
Go to UniProtKB:  Q6UWB1
GTEx:  ENSG00000104998 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6UWB1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.178α = 90
b = 99.903β = 90
c = 135.464γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2022-12-14 
  • Deposition Author(s): Gras, S.

Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1159272

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-01-03
    Changes: Database references