8W84

HLA-DQ2.5-alpha2 gliadin peptide in complex with DQN0344AE02


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.325 (Depositor), 0.330 (DCC) 
  • R-Value Work: 
    0.260 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.263 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Characterizations of a neutralizing antibody broadly reactive to multiple gluten peptide:HLA-DQ2.5 complexes in the context of celiac disease.

Okura, Y.Ikawa-Teranishi, Y.Mizoroki, A.Takahashi, N.Tsushima, T.Irie, M.Harfuddin, Z.Miura-Okuda, M.Ito, S.Nakamura, G.Takesue, H.Ozono, Y.Nishihara, M.Yamada, K.Gan, S.W.Hayasaka, A.Ishii, S.Wakabayashi, T.Muraoka, M.Nagaya, N.Hino, H.Nemoto, T.Kuramochi, T.Torizawa, T.Shimada, H.Kitazawa, T.Okazaki, M.Nezu, J.Sollid, L.M.Igawa, T.

(2023) Nat Commun 14: 8502-8502

  • DOI: https://doi.org/10.1038/s41467-023-44083-4
  • Primary Citation of Related Structures:  
    8W83, 8W84, 8W85, 8W86

  • PubMed Abstract: 

    In human celiac disease (CeD) HLA-DQ2.5 presents gluten peptides to antigen-specific CD4 + T cells, thereby instigating immune activation and enteropathy. Targeting HLA-DQ2.5 with neutralizing antibody for treating CeD may be plausible, yet using pan-HLA-DQ antibody risks affecting systemic immunity, while targeting selected gluten peptide:HLA-DQ2.5 complex (pHLA-DQ2.5) may be insufficient. Here we generate a TCR-like, neutralizing antibody (DONQ52) that broadly recognizes more than twenty-five distinct gluten pHLA-DQ2.5 through rabbit immunization with multi-epitope gluten pHLA-DQ2.5 and multidimensional optimization. Structural analyses show that the proline-rich and glutamine-rich motif of gluten epitopes critical for pathogenesis is flexibly recognized by multiple tyrosine residues present in the antibody paratope, implicating the mechanisms for the broad reactivity. In HLA-DQ2.5 transgenic mice, DONQ52 demonstrates favorable pharmacokinetics with high subcutaneous bioavailability, and blocks immunity to gluten while not affecting systemic immunity. Our results thus provide a rationale for clinical testing of DONQ52 in CeD.


  • Organizational Affiliation

    Translational Research Division, Chugai Pharmaceutical Co., Ltd., Tokyo, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DQN0344AE02 Fab heavy chain228Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DQN0344AE02 Fab light chain215Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DQ alpha 1 chain189Homo sapiensMutation(s): 1 
Gene Names: HLA-DQA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01909 (Homo sapiens)
Explore P01909 
Go to UniProtKB:  P01909
PHAROS:  P01909
GTEx:  ENSG00000196735 
Entity Groups  
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UniProt GroupP01909
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01909-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class II HLA-DQ-beta-1 - alpha2 gliadin peptide chimeric protein226Homo sapiensMutation(s): 0 
UniProt
Find proteins for O19712 (Homo sapiens)
Explore O19712 
Go to UniProtKB:  O19712
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO19712
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.325 (Depositor), 0.330 (DCC) 
  • R-Value Work:  0.260 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.263 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.86α = 90
b = 138.707β = 90
c = 201.928γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Database references
  • Version 1.3: 2024-10-09
    Changes: Structure summary