Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 44990.36 
• Atom Count: 2941 
• Residue Count: 382 
• Unique protein chains: 3

5JWD

Crystal structure of H-2Db in complex with the LCMV-derived GP392-401 peptide

• DOI: 10.2210/pdb5JWD/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Lymphocytic choriomeningitis virus (strain Armstrong)
• Expression System: Escherichia coli


• Deposited: 2016-05-12 Released: 2017-05-24 
• Deposition Author(s): Buratto, J., Badia-Martinez, D., Norstrom, M., Sandalova, T., Achour, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.229 
• R-Value Work: 0.180 

Literature

Crystal structures of H-2Db in complex with the LCMV-derived peptides GP92 and GP392 explain pleiotropic effects of glycosylation on antigen presentation and immunogenicity.

Hafstrand, I., Badia-Martinez, D., Josey, B.J., Norstrom, M., Buratto, J., Pellegrino, S., Duru, A.D., Sandalova, T., Achour, A.

(2017) PLoS ONE 12: e0189584-e0189584

• PubMed: 29253009 
• DOI: 10.1371/journal.pone.0189584
• Primary Citation of Related Structures:  
  5JWE


• PubMed Abstract: 
  

Post-translational modifications significantly broaden the epitope repertoire for major histocompatibility class I complexes (MHC-I) and may allow viruses to escape immune recognition. Lymphocytic choriomeningitis virus (LCMV) infection of H-2b mice generates CD8+ CTL responses directed towards several MHC-I-restricted epitopes including the peptides GP92 (CSANNSHHYI) and GP392 (WLVTNGSYL), both with a N-glycosylation site. Interestingly, glycosylation has different effects on the immunogenicity and association capacity of these two epitopes to H-2Db. To assess the structural bases underlying these functional results, we determined the crystal structures of H-2Db in complex with GP92 (CSANNSHHYI) and GP392 (WLVTNGSYL) to 2.4 and 2.5 Å resolution, respectively. The structures reveal that while glycosylation of GP392 most probably impairs binding, the glycosylation of the asparagine residue in GP92, which protrudes towards the solvent, possibly allows for immune escape and/or forms a neo-epitope that may select for a different set of CD8 T cells. Altogether, the presented results provide a structural platform underlying the effects of post-translational modifications on epitope binding and/or immunogenicity, resulting in viral immune escape.

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Organizational Affiliation: 

Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Department of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
H-2 class I histocompatibility antigen, D-B alpha chain	A	274	Mus musculus	Mutation(s): 0  Gene Names: H2-D1
Find proteins for P01899 (Mus musculus) Go to UniProtKB:  P01899

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B	99	Mus musculus	Mutation(s): 0  Gene Names: B2m
Find proteins for P01887 (Mus musculus) Go to UniProtKB:  P01887

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Pre-glycoprotein polyprotein GP complex	C	9	Lymphocytic choriomeningitis virus (strain Armstrong)	Mutation(s): 0  Gene Names: GPC (GP-C)
Find proteins for P09991 (Lymphocytic choriomeningitis virus (strain Armstrong)) Go to UniProtKB:  P09991

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.229 
• R-Value Work: 0.180 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 90.300	α = 90.00
b = 108.800	β = 121.90
c = 58.000	γ = 90.00

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-05-12 
• Released Date: 2017-05-24 
• Deposition Author(s): Buratto, J., Badia-Martinez, D., Norstrom, M., Sandalova, T., Achour, A.

Revision History 

• Version 1.0: 2017-05-24
  Type: Initial release
• Version 1.1: 2017-12-27
  Type: Database references