9EJH | pdb_00009ejh

Peptide-independent T cell receptor recognition of HLA-DQ2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.232 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A naturally selected alpha beta T cell receptor binds HLA-DQ2 molecules without co-contacting the presented peptide.

Lim, J.J.Jones, C.M.Loh, T.J.Dao, H.T.Tran, M.T.Tye-Din, J.A.La Gruta, N.L.Rossjohn, J.

(2025) Nat Commun 16: 3330-3330

  • DOI: https://doi.org/10.1038/s41467-025-58690-w
  • Primary Citation of Related Structures:  
    9EJG, 9EJH, 9EJI

  • PubMed Abstract: 

    αβ T cell receptors (TCR) co-recognise peptide (p) antigens that are presented by major histocompatibility complex (MHC) molecules. While marked variations in TCR-p-MHC docking topologies have been observed from structural studies, the co-recognition paradigm has held fast. Using HLA-DQ2.5-peptide tetramers, here we identify a TRAV12-1 + -TRBV5-1 + G9 TCR from human peripheral blood that binds HLA-DQ2.5 in a peptide-agnostic manner. The crystal structures of TCR-HLA-DQ2.5-peptide complexes show that the G9 TCR binds HLA-DQ2.5 in a reversed docking topology without contacting the peptide, with the TCR contacting the β1 region of HLA-DQ2.5 and distal from the peptide antigen binding cleft. High-throughput screening of HLA class I and II molecules finds the G9 TCR to be pan-HLA-DQ2 reactive, with leucine-55 of HLA-DQ2.5 being a key determinant underpinning G9 TCR specificity excluding other HLA-II allomorphs. Consistent with the functional assays, the interactions of the G9 TCR and HLA-DQ2.5 precludes CD4 binding, thereby impeding T cell activation. Collectively, we describe a naturally selected αβTCR from human peripheral blood that deviates from the TCR-p-MHC co-recognition paradigm.


  • Organizational Affiliation

    Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DQ alpha 1 chain183Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01909 (Homo sapiens)
Explore P01909 
Go to UniProtKB:  P01909
PHAROS:  P01909
GTEx:  ENSG00000196735 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01909
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01909-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class II HLA-DQ-beta-1194Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1
UniProt
Find proteins for O19712 (Homo sapiens)
Explore O19712 
Go to UniProtKB:  O19712
Entity Groups  
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UniProt GroupO19712
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen gamma chain13Homo sapiensMutation(s): 0 
Gene Names: CD74DHLAG
UniProt & NIH Common Fund Data Resources
Find proteins for P04233 (Homo sapiens)
Explore P04233 
Go to UniProtKB:  P04233
PHAROS:  P04233
GTEx:  ENSG00000019582 
Entity Groups  
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UniProt GroupP04233
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
G9 T cell receptor alpha chain204Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
G9 T cell receptor beta chain242Homo sapiensMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth B],
I [auth B],
K [auth E],
L [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.232 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.974α = 90
b = 43.272β = 90.312
c = 257.958γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Database references
  • Version 1.2: 2025-05-21
    Changes: Database references