1INQ

Structure of Minor Histocompatibility Antigen peptide, H13a, complexed to H2-Db


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

How H13 histocompatibility peptides differing by a single methyl group and lacking conventional MHC binding anchor motifs determine self-nonself discrimination.

Ostrov, D.A.Roden, M.M.Shi, W.Palmieri, E.Christianson, G.J.Mendoza, L.Villaflor, G.Tilley, D.Shastri, N.Grey, H.Almo, S.C.Roopenian, D.Nathenson, S.G.

(2002) J.Immunol. 168: 283-289

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The mouse H13 minor histocompatibility (H) Ag, originally detected as a barrier to allograft transplants, is remarkable in that rejection is a consequence of an extremely subtle interchange, P4(Val/Ile), in a nonamer H2-D(b)-bound peptide. Moreover, ...

    The mouse H13 minor histocompatibility (H) Ag, originally detected as a barrier to allograft transplants, is remarkable in that rejection is a consequence of an extremely subtle interchange, P4(Val/Ile), in a nonamer H2-D(b)-bound peptide. Moreover, H13 peptides lack the canonical P5(Asn) central anchor residue normally considered important for forming a peptide/MHC complex. To understand how these noncanonical peptide pMHC complexes form physiologically active TCR ligands, crystal structures of allelic H13 pD(b) complexes and a P5(Asn) anchored pD(b) analog were solved to high resolution. The structures show that the basis of TCRs to distinguish self from nonself H13 peptides is their ability to distinguish a single solvent-exposed methyl group. In addition, the structures demonstrate that there is no need for H13 peptides to derive any stabilization from interactions within the central C pocket to generate fully functional pMHC complexes. These results provide a structural explanation for a classical non-MHC-encoded H Ag, and they call into question the requirement for contact between anchor residues and the major MHC binding pockets in vaccine design.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, 1600 Morris Boulevard, Bronx, NY 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
A
275Mus musculusMutation(s): 0 
Gene Names: H2-D1
Find proteins for P01899 (Mus musculus)
Go to UniProtKB:  P01899
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
MHC Class I H13a minor histocompatibility peptide
C
9Mus musculusMutation(s): 0 
Gene Names: Hm13 (H13, Psl3)
EC: 3.4.23.-
Find proteins for Q9D8V0 (Mus musculus)
Go to UniProtKB:  Q9D8V0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.640α = 90.00
b = 109.420β = 120.01
c = 57.560γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance