5VCL

Structure of the Qdm peptide bound to Qa-1a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of Qa-1a with bound Qa-1 determinant modifier peptide.

Ying, G.Wang, J.Kumar, V.Zajonc, D.M.

(2017) PLoS ONE 12: e0182296-e0182296

  • DOI: 10.1371/journal.pone.0182296

  • PubMed Abstract: 
  • Qa-1 is a non-classical Major Histocompatibility (MHC) class I molecule that generally presents hydrophobic peptides including Qdm derived from the leader sequence of classical MHC I molecules for immune surveillance by NK cells. Qa-1 bound peptides ...

    Qa-1 is a non-classical Major Histocompatibility (MHC) class I molecule that generally presents hydrophobic peptides including Qdm derived from the leader sequence of classical MHC I molecules for immune surveillance by NK cells. Qa-1 bound peptides derived from the TCR Vβ8.2 of activated T cells also activates CD8+ regulatory T cells to control autoimmunity and maintain self-tolerance. Four allotypes of Qa-1 (Qa-1a-d) are expressed that are highly conserved in sequence but have several variations that could affect peptide binding to Qa-1 or TCR recognition. Here, we determined the structure of Qa-1a with bound Qdm peptide. While the overall structure is very similar to that of Qa-1b, there are several amino acid differences around the peptide binding platform that could affect TCR recognition. Most notably, two amino acid substitutions are found in the pocket P2, which binds the anchor residue Met2 of the Qdm peptide. These residues affect both the size and shape of the binding pocket, as well as affect the charge at physiologic pH, suggesting Qa-1a and Qa-1b could present slightly distinct peptide reservoirs, which could presumably be recognized by different populations of CD8+ T cells.


    Organizational Affiliation

    Division of Cell Biology, La Jolla Institute for Allergy and Immunology (LJI), La Jolla, California, United States of America.,Department of Medicine, University of California San Diego, La Jolla, California, United States of America.,Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H2-T23 protein
A
278Mus musculusMutation(s): 0 
Gene Names: H2-T23
Find proteins for Q31153 (Mus musculus)
Go to UniProtKB:  Q31153
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Qdm peptide
P
9Mus musculusMutation(s): 0 
Gene Names: H2-L
Find proteins for P01897 (Mus musculus)
Go to UniProtKB:  P01897
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.217 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 67.207α = 90.00
b = 75.876β = 90.00
c = 105.211γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-03-31 
  • Released Date: 2017-10-25 
  • Deposition Author(s): Ying, G., Zajonc, D.M.

Revision History 

  • Version 1.0: 2017-10-25
    Type: Initial release