5OQG

Crystal structure of a single chain trimer composed of the MHC I heavy chain H-2Kb W167A, beta-2microglobulin, and and ovalbumin-derived peptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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

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

(2018) J Biol Chem 293: 7538-7548

  • DOI: 10.1074/jbc.RA117.000313
  • Structures With Same Primary Citation

  • 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 pept ...

    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.


    Organizational Affiliation

    Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, United Kingdom.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain
A, B
431Mus musculusMutation(s): 1 
Gene Names: B2m
Find proteins for P01901 (Mus musculus)
Go to UniProtKB:  P01901
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.43α = 90
b = 89.64β = 111.24
c = 89.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United KingdomBB/L010402/1

Revision History 

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Derived calculations
  • Version 1.2: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.3: 2019-10-16
    Changes: Data collection