8W84 | pdb_00008w84

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), 0.326 (DCC) 
  • R-Value Work: 
    0.260 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 
    0.263 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 95.73 kDa 
  • Atom Count: 6,415 
  • Modeled Residue Count: 812 
  • Deposited Residue Count: 858 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DQN0344AE02 Fab heavy chain228Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DQN0344AE02 Fab light chain215Homo sapiensMutation(s): 0 
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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
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01909
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01909-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.325 (Depositor), 0.326 (DCC) 
  • R-Value Work:  0.260 (Depositor), 0.253 (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

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Ligand Structure Quality Assessment 


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
  • Version 1.4: 2026-03-04
    Changes: Refinement description