4GG8

Immune Receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report



Literature

Biased T Cell Receptor Usage Directed against Human Leukocyte Antigen DQ8-Restricted Gliadin Peptides Is Associated with Celiac Disease

Broughton, S.E.Petersen, J.Theodossis, A.Scally, S.W.Loh, K.L.Thompson, A.van Bergen, J.Kooy-Winkelaar, Y.Henderson, K.N.Beddoe, T.Tye-Din, J.A.Mannering, S.I.Purcell, A.W.McCluskey, J.Anderson, R.P.Koning, F.Reid, H.H.Rossjohn, J.

(2012) Immunity 

  • DOI: 10.1016/j.immuni.2012.07.013
  • Primary Citation of Related Structures:  
    4GG6, 4GG8

  • PubMed Abstract: 
  • Celiac disease is a human leukocyte antigen (HLA)-DQ2- and/or DQ8-associated T cell-mediated disorder that is induced by dietary gluten. Although it is established how gluten peptides bind HLA-DQ8 and HLA-DQ2, it is unclear how such peptide-HLA compl ...

    Celiac disease is a human leukocyte antigen (HLA)-DQ2- and/or DQ8-associated T cell-mediated disorder that is induced by dietary gluten. Although it is established how gluten peptides bind HLA-DQ8 and HLA-DQ2, it is unclear how such peptide-HLA complexes are engaged by the T cell receptor (TCR), a recognition event that triggers disease pathology. We show that biased TCR usage (TRBV9(∗)01) underpins the recognition of HLA-DQ8-α-I-gliadin. The structure of a prototypical TRBV9(∗)01-TCR-HLA-DQ8-α-I-gliadin complex shows that the TCR docks centrally above HLA-DQ8-α-I-gliadin, in which all complementarity-determining region-β (CDRβ) loops interact with the gliadin peptide. Mutagenesis at the TRBV9(∗)01-TCR-HLA-DQ8-α-I-gliadin interface provides an energetic basis for the Vβ bias. Moreover, CDR3 diversity accounts for TRBV9(∗)01(+) TCRs exhibiting differing reactivities toward the gliadin epitopes at various deamidation states. Accordingly, biased TCR usage is an important factor in the pathogenesis of DQ8-mediated celiac disease.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T-CELL RECEPTOR, SP3.4 ALPHA CHAINAE207Homo sapiensMutation(s): 0 
Find proteins for K7N5N2 (Homo sapiens)
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Go to UniProtKB:  K7N5N2
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
T-CELL RECEPTOR, SP3.4 BETA CHAINBF245Homo sapiensMutation(s): 0 
Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens)
Explore P01850 
Go to UniProtKB:  P01850
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
C, D
2 N/A Oligosaccharides Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
C, DsucroseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.265 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.562α = 90
b = 124.562β = 90
c = 61.098γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary