8V51 | pdb_00008v51

Crystal structure of a HLA-B*35:01-NP10 with D1 TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.244 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular determinants of cross-strain influenza A virus recognition by alpha beta T cell receptors.

Quinones-Parra, S.M.Gras, S.Nguyen, T.H.O.Farenc, C.Szeto, C.Rowntree, L.C.Chaurasia, P.Sant, S.Boon, A.C.M.Jayasinghe, D.Rimmelzwaan, G.F.Petersen, J.Doherty, P.C.Uldrich, A.P.Littler, D.R.Rossjohn, J.Kedzierska, K.

(2025) Sci Immunol 10: eadn3805-eadn3805

  • DOI: https://doi.org/10.1126/sciimmunol.adn3805
  • Primary Citation of Related Structures:  
    8V4Z, 8V50, 8V51

  • PubMed Abstract: 

    Cross-reactive αβ T cell receptors (TCRs) recognizing multiple peptide variants can provide effective control of rapidly evolving viruses yet remain understudied. By screening 12 naturally occurring influenza-derived HLA-B*35:01-restricted nucleoprotein (NP) 418-426 epitopes (B*35:01-NP 418 ) that emerged since 1918 within influenza A viruses, including 2024 A/H5N1 viruses, we identified functional broadly cross-reactive T cells universally recognizing NP 418 variants. Binding studies demonstrated that TCR cross-reactivity was concomitant with diminished antigen sensitivity. Primary human B*35:01/NP 418 + CD8 + T cell lines displayed reduced cross-reactivity in the absence of CD8 coreceptor binding, validating the low avidity of cross-reactive B*35:01-NP 418 + CD8 + T cell responses. Six TCR-HLA-B*35:01/NP 418 crystal structures showed how cross-reactive TCRs recognized multiple B*35:01/NP 418 epitope variants. Specific TCR interactions were formed with invariant and conserved peptide-HLA features, thus remaining distal from highly varied positions of the NP 418 epitope. Our study defines molecular mechanisms associated with extensive TCR cross-reactivity toward naturally occurring viral variants highly relevant to universal protective immunity against influenza.


  • Organizational Affiliation
    • Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA-B35273Homo sapiensMutation(s): 0 
Gene Names: B-3501
UniProt
Find proteins for O19626 (Homo sapiens)
Explore O19626 
Go to UniProtKB:  O19626
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UniProt GroupO19626
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Homo sapiensMutation(s): 0 
Gene Names: B2M
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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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
LEU-PRO-PHE-GLU-LYS-SER-THR-VAL-MET9Influenza A virusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
D1 TCR alpha chain198Homo sapiensMutation(s): 0 
Gene Names: TRAV1*01
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
D1 TCR beta chain242Homo sapiensMutation(s): 0 
Gene Names: TRBV7-8*01
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth A],
I [auth D],
J [auth D],
K [auth E],
L [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.244 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.269α = 90
b = 46.155β = 101.402
c = 161.964γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
  • Version 1.1: 2025-02-26
    Changes: Database references