Skip to main content

 8RLU | pdb_00008rlu

TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 S3N peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.261 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.214 (DCC) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8RLU

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 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.

Macromolecule Content 

  • Total Structure Weight: 188.25 kDa 
  • Atom Count: 13,115 
  • Modeled Residue Count: 1,605 
  • Deposited Residue Count: 1,654 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, alpha chain E
A, F
276Homo sapiensMutation(s): 0 
Gene Names: HLA-E, HLA-6.2, HLAE
UniProt & NIH Common Fund Data Resources
Find proteins for P13747 (Homo sapiens)
Explore P13747 
Go to UniProtKB:  P13747
PHAROS:  P13747
GTEx:  ENSG00000204592 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13747
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, G
100Homo 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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Large envelope protein
C, H
9Hepatitis B virusMutation(s): 1 
UniProt
Find proteins for Q67953 (Hepatitis B virus)
Explore Q67953 
Go to UniProtKB:  Q67953
Entity Groups
UniProt GroupQ67953
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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: TRAV12-2, TRA
UniProt & NIH Common Fund Data Resources
Find proteins for A0A075B6T6 (Homo sapiens)
Explore A0A075B6T6 
Go to UniProtKB:  A0A075B6T6
PHAROS:  A0A075B6T6
GTEx:  ENSG00000211789 
Find proteins for P0DTU3 (Homo sapiens)
Explore P0DTU3 
Go to UniProtKB:  P0DTU3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0DTU3A0A075B6T6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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: TRBV6-5, TRB
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0K0K1A5 (Homo sapiens)
Explore A0A0K0K1A5 
Go to UniProtKB:  A0A0K0K1A5
PHAROS:  A0A0K0K1A5
GTEx:  ENSG00000211721 
Find proteins for P0DTU4 (Homo sapiens)
Explore P0DTU4 
Go to UniProtKB:  P0DTU4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0DTU4A0A0K0K1A5
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.261 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.214 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.417α = 90
b = 147.845β = 99.026
c = 91.908γ = 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