3DXA

Crystal Structure of the DM1 TCR in complex with HLA-B*4405 and decamer EBV antigen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.289 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Natural micropolymorphism in human leukocyte antigens provides a basis for genetic control of antigen recognition.

Archbold, J.K.Macdonald, W.A.Gras, S.Ely, L.K.Miles, J.J.Bell, M.J.Brennan, R.M.Beddoe, T.Wilce, M.C.Clements, C.S.Purcell, A.W.McCluskey, J.Burrows, S.R.Rossjohn, J.

(2009) J Exp Med 206: 209-219

  • DOI: 10.1084/jem.20082136
  • Primary Citation of Related Structures:  
    3DXA, 3DX7, 3DX8, 3DX9, 3DX6

  • PubMed Abstract: 
  • Human leukocyte antigen (HLA) gene polymorphism plays a critical role in protective immunity, disease susceptibility, autoimmunity, and drug hypersensitivity, yet the basis of how HLA polymorphism influences T cell receptor (TCR) recognition is uncle ...

    Human leukocyte antigen (HLA) gene polymorphism plays a critical role in protective immunity, disease susceptibility, autoimmunity, and drug hypersensitivity, yet the basis of how HLA polymorphism influences T cell receptor (TCR) recognition is unclear. We examined how a natural micropolymorphism in HLA-B44, an important and large HLA allelic family, affected antigen recognition. T cell-mediated immunity to an Epstein-Barr virus determinant (EENLLDFVRF) is enhanced when HLA-B*4405 was the presenting allotype compared with HLA-B*4402 or HLA-B*4403, each of which differ by just one amino acid. The micropolymorphism in these HLA-B44 allotypes altered the mode of binding and dynamics of the bound viral epitope. The structure of the TCR-HLA-B*4405(EENLLDFVRF) complex revealed that peptide flexibility was a critical parameter in enabling preferential engagement with HLA-B*4405 in comparison to HLA-B*4402/03. Accordingly, major histocompatibility complex (MHC) polymorphism can alter the dynamics of the peptide-MHC landscape, resulting in fine-tuning of T cell responses between closely related allotypes.


    Organizational Affiliation

    The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility complex HLA-B*4402AFK276Homo sapiensMutation(s): 1 
Gene Names: HLA-BHLAB
Find proteins for P01889 (Homo sapiens)
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Go to UniProtKB:  P01889
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PHAROS  P01889
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBGL99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
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Go to UniProtKB:  P61769
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PHAROS  P61769
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
EBV decapeptide epitopeCHM10N/AMutation(s): 0 
Find proteins for P03204 (Epstein-Barr virus (strain B95-8))
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Go to UniProtKB:  P03204
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DM1 T cell receptor alpha chainDIN199Homo sapiensMutation(s): 0 
Gene Names: TRACTCRA
Find proteins for P01848 (Homo sapiens)
Explore P01848 
Go to UniProtKB:  P01848
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PHAROS  P01848
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DM1 T cell receptor beta chainEJO244Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.289 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.954α = 90
b = 121.954β = 90
c = 695.914γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance