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 7T5M | pdb_00007t5m

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 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7T5M

This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 92.21 kDa 
  • Atom Count: 8,060 
  • Modeled Residue Count: 783 
  • Deposited Residue Count: 794 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  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
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UniProt GroupQ861F7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, D
99Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  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
PHAROS:  Q6UWB1
GTEx:  ENSG00000104998 
Entity Groups
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UniProt GroupQ6UWB1
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free:  0.208 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
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
  • Version 1.3: 2024-10-23
    Changes: Structure summary