3DXA | pdb_00003dxa

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 (Depositor), 0.318 (DCC) 
  • R-Value Work: 
    0.286 (Depositor), 0.282 (DCC) 
  • R-Value Observed: 
    0.289 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 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 Medicine 206: 209-219

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

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 286.36 kDa 
  • Atom Count: 20,171 
  • Modeled Residue Count: 2,484 
  • Deposited Residue Count: 2,484 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility complex HLA-B*4402
A, F, K
276Homo sapiensMutation(s): 1 
Gene Names: HLA-BHLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens)
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Go to UniProtKB:  P01889
PHAROS:  P01889
GTEx:  ENSG00000234745 
Entity Groups
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UniProt GroupP01889
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, G, L
99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
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Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
EBV decapeptide epitope
C, H, M
10N/AMutation(s): 0 
UniProt
Find proteins for P03204 (Epstein-Barr virus (strain B95-8))
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UniProt GroupP03204
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DM1 T cell receptor alpha chain
D, I, N
199Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens)
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PHAROS:  P01848
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UniProt GroupP01848
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DM1 T cell receptor beta chain
E, J, O
244Homo sapiensMutation(s): 0 
UniProt
Find proteins for P01850 (Homo sapiens)
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UniProt GroupP01850
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.330 (Depositor), 0.318 (DCC) 
  • R-Value Work:  0.286 (Depositor), 0.282 (DCC) 
  • R-Value Observed: 0.289 (Depositor) 
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  (Full details and data files)

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary