3SJV

Crystal structure of the RL42 TCR in complex with HLA-B8-FLR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

A structural basis for varied alpha-beta TCR usage against an immunodominant EBV antigen restricted to a HLA-B8 molecule.

Gras, S., Wilmann, P.G., Chen, Z., Halim, H., Liu, Y.C., Kjer-Nielsen, L., Purcell, A.W., Burrows, S.R., McCluskey, J., Rossjohn, J.

(2012) J Immunol 188: 311-321

  • DOI: https://doi.org/10.4049/jimmunol.1102686
  • Primary Citation of Related Structures:  
    3SJV, 3SKM, 3SKN, 3SKO

  • PubMed Abstract: 

    • EBV is a ubiquitous and persistent human pathogen, kept in check by the cytotoxic T cell response. In this study, we investigated how three TCRs, which differ in their T cell immunodominance hierarchies and gene usage, interact with the same EBV determinant (FLRGRAYGL), bound to the same Ag-presenting molecule, HLA-B8 ...

    EBV is a ubiquitous and persistent human pathogen, kept in check by the cytotoxic T cell response. In this study, we investigated how three TCRs, which differ in their T cell immunodominance hierarchies and gene usage, interact with the same EBV determinant (FLRGRAYGL), bound to the same Ag-presenting molecule, HLA-B8. We found that the three TCRs exhibit differing fine specificities for the viral Ag. Further, via structural and biophysical approaches, we demonstrated that the viral Ag provides the greatest energetic contribution to the TCR-peptide-HLA interaction, while focusing on a few adjacent HLA-based interactions to further tune fine-specificity requirements. Thus, the TCR engages the peptide-HLA with the viral Ag as the main glue, such that neighboring TCR-MHC interactions are recruited as a supportive adhesive. Collectively, we provide a portrait of how the host's adaptive immune response differentially engages a common viral Ag.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-8 alpha chain
A, F, K, P
277Homo sapiensMutation(s): 0 
Gene Names: HLA-B, HLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens)
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PHAROS:  P01889
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UniProt GroupP01889
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, G, L, Q
100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
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Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
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UniProt GroupP61769
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Epstein-Barr nuclear antigen 3
C, H, M, R
9Human gammaherpesvirus 4Mutation(s): 0 
Gene Names: EBNA3, BLRF3-BERF1
UniProt
Find proteins for Q3KST2 (Epstein-Barr virus (strain GD1))
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UniProt GroupQ3KST2
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RL42 T cell receptor, alpha chain
D, I, N, S
203Homo sapiensMutation(s): 0 
Gene Names: TRAC, TCRA
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Find proteins for P01848 (Homo sapiens)
Explore P01848 
Go to UniProtKB:  P01848
PHAROS:  P01848
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UniProt GroupP01848
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RL42 T cell receptor, beta chain
E, J, O, T
244Homo sapiensMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.08α = 90
b = 185β = 90
c = 217.68γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2012-08-01
    Changes: Structure summary
  • Version 1.2: 2020-02-05
    Changes: Advisory, Database references, Derived calculations
  • Version 1.3: 2023-09-13
    Changes: Advisory, Data collection, Database references, Refinement description