3SJV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.4049/jimmunol.1102686
  • Primary Citation of Related Structures:  

  • 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 dete ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, B-8 alpha chain
A, F, K, P
277Homo sapiensMutation(s): 0 
Gene Names: HLA-B (HLAB)
Find proteins for P30460 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P30460
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, G, L, Q
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Epstein-Barr nuclear antigen 3
C, H, M, R
9Epstein-Barr virus (strain GD1)Mutation(s): 0 
Gene Names: EBNA3
Find proteins for Q3KST2 (Epstein-Barr virus (strain GD1))
Go to UniProtKB:  Q3KST2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RL42 T cell receptor, alpha chain
D, I, N, S
203Homo sapiensMutation(s): 0 
Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RL42 T cell receptor, beta chain
E, J, O, T
244N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.253 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 100.080α = 90.00
b = 185.000β = 90.00
c = 217.680γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2012-08-01
    Type: Structure summary