5OQF

Crystal structure of a single chain trimer composed of the MHC 1 heavy chain H2-Kb WT, beta-2microglobulin, and ovalbumin derived peptide

Summary for 5OQF

• Entry DOI: 10.2210/pdb5oqf/pdb
• Descriptor: Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain (2 entities in total)
• Functional Keywords: diagnosis, epitopes, major histocompatibility complex, mice, models, molecular conformation, peptides, receptors, antigen, t-cell, t-lymphocytes, vaccines, immune system
• Biological source: Mus musculus (Mouse); More
• Total number of polymer chains: 2
• Total formula weight: 96363.22

Authors

Mikolajek, H.,Werner, J.M. (deposition date: 2017-08-11, release date: 2018-04-11, Last modification date: 2024-01-17)

Primary citation

Papakyriakou, A.,Reeves, E.,Beton, M.,Mikolajek, H.,Douglas, L.,Cooper, G.,Elliott, T.,Werner, J.M.,James, E.
The partial dissociation of MHC class I-bound peptides exposes their N terminus to trimming by endoplasmic reticulum aminopeptidase 1.
J. Biol. Chem., 293:7538-7548, 2018

PubMed Abstract: Endoplasmic reticulum aminopeptidase 1 (ERAP1) and ERAP2 process N-terminally extended antigenic precursors for optimal loading onto major histocompatibility complex class I (MHC I) molecules. We and others have demonstrated that ERAP1 processes peptides bound to MHC I, but the underlying mechanism is unknown. To this end, we utilized single-chain trimers (SCT) of the ovalbumin-derived epitope SIINFEKL (SL8) tethered to the H2-K MHC I determinant from mouse and introduced three substitutions, E63A, K66A, and W167A, at the A-pocket of the peptide-binding groove in the MHC I heavy chain, which interact with the N termini of peptides. These variants significantly decreased SL8-presenting SCT at the cell surface in the presence of ERAP1, but did not affect overall SCT expression, indicating that ERAP1 trims the SL8 N terminus. Comparison of the X-ray crystal structures of WT and three variant SCTs revealed only minor perturbations of the peptide-binding domain in the variants. However, molecular dynamics simulations suggested that SL8 can dissociate partially within a sub-microsecond timescale, exposing its N terminus to the solvent. We also found that the C terminus of MHC I-bound SL8 remains deeply buried in the F-pocket of MHC I. Furthermore, free-energy calculations revealed that the three SCT variants exhibit lower free-energy barriers of N terminus dissociation than the WT K Taken together, our results are consistent with a previously observed model in which the partial dissociation of bound peptides from MHC I exposes their N terminus to trimming by ERAP1, whereas their C terminus is anchored at the F-pocket.

PubMed: 29599287
DOI: 10.1074/jbc.RA117.000313

Experimental method

X-RAY DIFFRACTION (2.27 Å)