PDBsum entry 5oqh

Immune system

PDB id: 5oqh

Contents

Protein chains

388 a.a.

Waters ×462

PDB id:

5oqh

Name:

Immune system

Title:

Crystal structure of a disulfide trapped single chain trimer composed of the mhc i heavy chain h-2kb y84c k66a mutant, beta-2microglobulin, and ovalbumin-derived peptide

Structure:

Beta-2-microglobulin,h-2 class i histocompatibility antigen, k-b alpha chain. Chain: a, b. Synonym: h-2k(b). Engineered: yes

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: b2m, h2-k1, h2-k. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008

Resolution:

2.05Å R-factor: 0.207 R-free: 0.242

Authors:

H.Mikolajek,J.M.Werner,M.E.Beton

Key ref:

A.Papakyriakou et al. (2018). 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. PubMed id: 29599287 DOI: 10.1074/jbc.RA117.000313

Date:

11-Aug-17 Release date: 18-Apr-18

Protein chains

P01887  (B2MG_MOUSE) -  Beta-2-microglobulin from Mus musculus

Seq: 119 a.a.

Struc: 388 a.a.*

Protein chains

P01901  (HA1B_MOUSE) -  H-2 class I histocompatibility antigen, K-B alpha chain from Mus musculus

Seq: 369 a.a.

Struc: 388 a.a.*

* PDB and UniProt seqs differ at 35 residue positions (black crosses)

DOI no: 10.1074/jbc.RA117.000313

J Biol Chem 293:7538-7548 (2018)

PubMed id: 29599287

The partial dissociation of MHC class I-bound peptides exposes their N terminus to trimming by endoplasmic reticulum aminopeptidase 1.

A.Papakyriakou, E.Reeves, M.Beton, H.Mikolajek, L.Douglas, G.Cooper, T.Elliott, J.M.Werner, E.James.

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^b 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^b 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.