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: 3.5 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.286 

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:  

  • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility complex HLA-B*4402
A, F, K
276Homo sapiensMutation(s): 1 
Gene Names: HLA-B (HLAB)
Find proteins for P30481 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P30481
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, G, L
99Homo 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
EBV decapeptide epitope
C, H, M
10Epstein-Barr virus (strain B95-8)Mutation(s): 0 
Gene Names: EBNA6
Find proteins for P03204 (Epstein-Barr virus (strain B95-8))
Go to UniProtKB:  P03204
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DM1 T cell receptor alpha chain
D, I, N
199Homo sapiensMutation(s): 0 
Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DM1 T cell receptor beta chain
E, J, O
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: 3.5 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.286 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 121.954α = 90.00
b = 121.954β = 90.00
c = 695.914γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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