8RLT | pdb_00008rlt

TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 index peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.252 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.222 (DCC) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Viral sequence determines HLA-E-restricted T cell recognition of hepatitis B surface antigen.

Murugesan, G.Paterson, R.L.Kulkarni, R.Ilkow, V.Suckling, R.J.Connolly, M.M.Karuppiah, V.Pengelly, R.Jadhav, A.Donoso, J.Heunis, T.Bunjobpol, W.Philips, G.Ololade, K.Kay, D.Sarkar, A.Barber, C.Raj, R.Perot, C.Grant, T.Treveil, A.Walker, A.Dembek, M.Gibbs-Howe, D.Hock, M.Carreira, R.J.Atkin, K.E.Dorrell, L.Knox, A.Leonard, S.Salio, M.Godinho, L.F.

(2024) Nat Commun 15: 10126-10126

  • DOI: https://doi.org/10.1038/s41467-024-54378-9
  • Primary Citation of Related Structures:  
    8RLT, 8RLU, 8RLV

  • PubMed Abstract: 

    The non-polymorphic HLA-E molecule offers opportunities for new universal immunotherapeutic approaches to chronic infectious diseases. Chronic Hepatitis B virus (HBV) infection is driven in part by T cell dysfunction due to elevated levels of the HBV envelope (Env) protein hepatitis B surface antigen (HBsAg). Here we report the characterization of three genotypic variants of an HLA-E-binding HBsAg peptide, Env 371-379, identified through bioinformatic predictions and verified by biochemical and cellular assays. Using a soluble affinity-enhanced T cell receptor (TCR) (a09b08)-anti-CD3 bispecific molecule to probe HLA-E presentation of the Env 371-379 peptides, we demonstrate that only the most stable Env 371-379 variant, L6I, elicits functional responses to a09b08-anti-CD3-redirected polyclonal T cells co-cultured with targets expressing endogenous HBsAg. Furthermore, HLA-E-Env 371-379 L6I-specific CD8 + T cells are detectable in HBV-naïve donors and people with chronic HBV after in vitro priming. In conclusion, we provide evidence for HLA-E-mediated HBV Env peptide presentation, and highlight the effect of viral mutations on the stability and targetability of pHLA-E molecules.


  • Organizational Affiliation
    • Immunocore Ltd, 92 Park Drive, Abingdon, Oxfordshire, OX14 4RY, UK.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, alpha chain E
A, F
276Homo sapiensMutation(s): 0 
Gene Names: HLA-EHLA-6.2HLAE
UniProt & NIH Common Fund Data Resources
Find proteins for P13747 (Homo sapiens)
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PHAROS:  P13747
GTEx:  ENSG00000204592 
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UniProt GroupP13747
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, G
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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Find proteins for P61769 (Homo sapiens)
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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
Large envelope protein
C, H
9Hepatitis B virusMutation(s): 0 
UniProt
Find proteins for Q67953 (Hepatitis B virus)
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UniProt GroupQ67953
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5
D, I
199Homo sapiensMutation(s): 24 
Gene Names: TRAV12-2TRA
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Find proteins for A0A075B6T6 (Homo sapiens)
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PHAROS:  A0A075B6T6
GTEx:  ENSG00000211789 
Find proteins for P0DTU3 (Homo sapiens)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5
E, J
243Homo sapiensMutation(s): 17 
Gene Names: TRBV6-5TRB
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PHAROS:  A0A0K0K1A5
GTEx:  ENSG00000211721 
Find proteins for P0DTU4 (Homo sapiens)
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UniProt GroupsP0DTU4A0A0K0K1A5
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.252 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.222 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.698α = 90
b = 155.061β = 97.043
c = 93.414γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Database references