8W84

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

• PDB DOI: https://doi.org/10.2210/pdb8W84/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2023-08-31 Released: 2023-11-08 
• Deposition Author(s): Irie, M., Tsushima, T., Teranishi-Ikawa, Y., Takahashi, N., Ishii, S., Okura, Y., Fukami, T.A., Torizawa, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.325 
• R-Value Work: 0.260 
• R-Value Observed: 0.263 

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

• DOI: https://doi.org/10.1038/s41467-023-44083-4

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DQN0344AE02 Fab heavy chain	A	228	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DQN0344AE02 Fab light chain	B	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DQ alpha 1 chain	C	189	Homo sapiens	Mutation(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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II HLA-DQ-beta-1 - alpha2 gliadin peptide chimeric protein	D	226	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for O19712 (Homo sapiens) Explore O19712  Go to UniProtKB:  O19712

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth C], F [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.325 
• R-Value Work: 0.260 
• R-Value Observed: 0.263 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.86	α = 90
b = 138.707	β = 90
c = 201.928	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-08 
Deposition Author(s): Irie, M., Tsushima, T., Teranishi-Ikawa, Y., Takahashi, N., Ishii, S., Okura, Y., Fukami, T.A., Torizawa, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-11-08
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Database references