2FYY | pdb_00002fyy

The role of T cell receptor alpha genes in directing human MHC restriction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.236 (Depositor), 0.295 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.279 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history

Literature

TCR alpha genes direct MHC restriction in the potent human T cell response to a class I-bound viral epitope.

Miles, J.J.Borg, N.A.Brennan, R.M.Tynan, F.E.Kjer-Nielsen, L.Silins, S.L.Bell, M.J.Burrows, J.M.McCluskey, J.Rossjohn, J.Burrows, S.R.

(2006) J Immunol 177: 6804-6814

  • DOI: https://doi.org/10.4049/jimmunol.177.10.6804
  • Primary Citation Related Structures: 
    2FYY, 2FZ3

  • PubMed Abstract: 

    The underlying generic properties of alphabeta TCRs that control MHC restriction remain largely unresolved. To investigate MHC restriction, we have examined the CTL response to a viral epitope that binds promiscuously to two human leukocyte Ags (HLAs) that differ by a single amino acid at position 156. Individuals expressing either HLA-B*3501 (156Leucine) or HLA-B*3508 (156Arginine) showed a potent CTL response to the 407HPVGEADYFEY417 epitope from EBV. Interestingly, the response was characterized by highly restricted TCR beta-chain usage in both HLA-B*3501+ and HLA-B*3508+ individuals; however, this conserved TRBV9+ beta-chain was associated with distinct TCR alpha-chains depending upon the HLA-B*35 allele expressed by the virus-exposed host. Functional assays confirmed that TCR alpha-chain usage determined the HLA restriction of the CTLs. Structural studies revealed significant differences in the mobility of the peptide when bound to HLA-B*3501 or HLA-B*3508. In HLA-B*3501, the bulged section of the peptide was disordered, whereas in HLA-B*3508 the bulged epitope adopted an ordered conformation. Collectively, these data demonstrate not only that mobile MHC-bound peptides can be highly immunogenic but can also stimulate an extremely biased TCR repertoire. In addition, TCR alpha-chain usage is shown to play a critical role in controlling MHC restriction between closely related allomorphs.


  • Organizational Affiliation
    • Cellular Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, Australia.

Macromolecule Content 

  • Total Structure Weight: 45.02 kDa 
  • Atom Count: 3,433 
  • Modeled Residue Count: 382 
  • Deposited Residue Count: 386 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-35 alpha chain276Homo sapiensMutation(s): 0 
UniProt
Find proteins for O19626 (Homo sapiens)
Explore O19626 
Go to UniProtKB:  O19626
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UniProt GroupO19626
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Homo sapiensMutation(s): 0 
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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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
11-mer peptide from Epstein-Barr nuclear antigen 111N/AMutation(s): 0 
EC: 3.1.21
UniProt
Find proteins for P03211 (Epstein-Barr virus (strain B95-8))
Explore P03211 
Go to UniProtKB:  P03211
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UniProt GroupP03211
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.236 (Depositor), 0.295 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.279 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.045α = 90
b = 81.783β = 90
c = 110.308γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-10-09
    Changes: Structure summary