1INQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 

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

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

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAINA275Mus musculusMutation(s): 0 
Gene Names: H2-DbH2-D1
Find proteins for P01899 (Mus musculus)
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Go to UniProtKB:  P01899
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-2 MICROGLOBULINB99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MHC Class I H13a minor histocompatibility peptideC9N/AMutation(s): 0 
Find proteins for Q9D8V0 (Mus musculus)
Explore Q9D8V0 
Go to UniProtKB:  Q9D8V0
NIH Common Fund Data Resources
IMPC  MGI:95886
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

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: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.64α = 90
b = 109.42β = 120.01
c = 57.56γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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