Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 47.66 kDa 
• Atom Count: 3052 
• Modelled Residue Count: 372 
• Deposited Residue Count: 416 
• Unique protein chains: 2

6MFF

HLA-DQ2-glia-omega1

• DOI: 10.2210/pdb6MFF/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2018-09-10 Released: 2018-11-21 
• Deposition Author(s): Petersen, J., Ciacchi, L., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.250 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Literature

Discriminative T-cell receptor recognition of highly homologous HLA-DQ2-bound gluten epitopes.

Dahal-Koirala, S., Ciacchi, L., Petersen, J., Risnes, L.F., Neumann, R.S., Christophersen, A., Lundin, K.E.A., Reid, H.H., Qiao, S.W., Rossjohn, J., Sollid, L.M.

(2019) J Biol Chem 294: 941-952

• PubMed: 30455354 
• DOI: 10.1074/jbc.RA118.005736
• Primary Citation of Related Structures:  
  6MFG, 6MFF


• PubMed Abstract: 
  

Celiac disease (CeD) provides an opportunity to study the specificity underlying human T-cell responses to an array of similar epitopes presented by the same human leukocyte antigen II (HLA-II) molecule. Here, we investigated T-cell responses to the two immunodominant and highly homologous HLA-DQ2.5-restricted gluten epitopes, DQ2.5-glia-α1a (PFPQPELPY) and DQ2.5-glia-ω1 (PFPQPEQPF). Using HLA-DQ2.5-DQ2.5-glia-α1a and HLA-DQ2.5-DQ2.5-glia-ω1 tetramers and single-cell αβ T-cell receptor (TCR) sequencing, we observed that despite similarity in biased variable-gene usage in the TCR repertoire responding to these nearly identical peptide-HLA-II complexes, most of the T cells are specific for either of the two epitopes. To understand the molecular basis of this exquisite fine specificity, we undertook Ala substitution assays revealing that the p7 residue (Leu/Gln) is critical for specific epitope recognition by both DQ2.5-glia-α1a- and DQ2.5-glia-ω1-reactive T-cell clones. We determined high-resolution binary crystal structures of HLA-DQ2.5 bound to DQ2.5-glia-α1a (2.0 Å) and DQ2.5-glia-ω1 (2.6 Å). These structures disclosed that differences around the p7 residue subtly alter the neighboring substructure and electrostatic properties of the HLA-DQ2.5-peptide complex, providing the fine specificity underlying the responses against these two highly homologous gluten epitopes. This study underscores the ability of TCRs to recognize subtle differences in the peptide-HLA-II landscape in a human disease setting.

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Organizational Affiliation: 

the K. G. Jebsen Centre for Coeliac Disease Research, University of Oslo, 0424 Oslo, Norway.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DQ alpha 1 chain	A	190	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DQA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01909 (Homo sapiens) Explore P01909  Go to UniProtKB:  P01909
PHAROS:  P01909

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II HLA-DQ-beta-1 - DQ2-glia-omega1 chimeric protein	B [auth C]	226	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DQB1
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	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.250 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.87	α = 90
b = 96.61	β = 90
c = 107.05	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-09-10 
• Released Date: 2018-11-21 
Deposition Author(s): Petersen, J., Ciacchi, L., Rossjohn, J.

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2018-12-12
  Changes: Data collection, Database references
• Version 1.2: 2019-01-30
  Changes: Data collection, Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary