1JUF

Structure of Minor Histocompatibility Antigen peptide, H13b, complexed to H2-Db


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.4 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

  • DOI: https://doi.org/10.4049/jimmunol.168.1.283
  • Primary Citation of Related Structures:  
    1INQ, 1JUF

  • 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, 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H2-Db major histocompatibility antigen276Mus musculusMutation(s): 0 
Gene Names: H2-D
UniProt
Find proteins for P01899 (Mus musculus)
Explore P01899 
Go to UniProtKB:  P01899
Entity Groups  
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UniProt GroupP01899
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Mus musculusMutation(s): 0 
Gene Names: beta-2-microglobulin
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
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UniProt GroupP01887
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
H13b peptide9Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D8V0 (Mus musculus)
Explore Q9D8V0 
Go to UniProtKB:  Q9D8V0
IMPC:  MGI:95886
Entity Groups  
UniProt GroupQ9D8V0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.997α = 90
b = 109.707β = 120.52
c = 57.654γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2016-05-25
    Changes: Database references, Source and taxonomy
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Refinement description