1IAO

CLASS II MHC I-AD IN COMPLEX WITH OVALBUMIN PEPTIDE 323-339


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of two I-Ad-peptide complexes reveal that high affinity can be achieved without large anchor residues.

Scott, C.A.Peterson, P.A.Teyton, L.Wilson, I.A.

(1998) Immunity 8: 319-329

  • Primary Citation of Related Structures:  2IAD

  • PubMed Abstract: 
  • We have determined the structures of I-Ad covalently linked to an ovalbumin peptide (OVA323-339) and to an influenza virus hemagglutinin peptide (HA126-138). The floor of the peptide-binding groove contains an unusual beta bulge, not seen in I-E and ...

    We have determined the structures of I-Ad covalently linked to an ovalbumin peptide (OVA323-339) and to an influenza virus hemagglutinin peptide (HA126-138). The floor of the peptide-binding groove contains an unusual beta bulge, not seen in I-E and DR structures, that affects numerous interactions between the alpha and beta chains and bound peptide. Unlike other MHC-peptide complexes, the peptides do not insert any large anchor residues into the binding pockets of the shallow I-Ad binding groove. The previously identified six-residue "core" binding motif of I-Ad occupies only the P4 to P9 pockets, implying that specificity of T cell receptor recognition of I-Ad-peptide complexes can be accomplished by peptides that only partially fill the MHC groove.


    Related Citations: 
    • Role of Chain Pairing for the Production of Functional Soluble Ia Major Histocompatibility Complex Class II Molecules
      Scott, C.A.,Garcia, K.C.,Carbone, F.R.,Wilson, I.A.,Teyton, L.
      (1996) J.Exp.Med. 183: 2087
    • Engineering Protein for X-Ray Crystallography: The Murine Major Histocompatibility Complex Class II Molecule I-Ad
      Scott, C.A.,Garcia, K.C.,Stura, E.A.,Peterson, P.A.,Wilson, I.A.,Teyton, L.
      (1998) Protein Sci. 7: 413
    • Erratum. Crystal Structures of Two I-Ad-Peptide Complexes Reveal that High Affinity Can be Achieved without Large Anchor Residues
      Scott, C.A.,Peterson, P.A.,Teyton, L.,Wilson, I.A.
      (1998) Immunity 8: 531


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS II I-AD
A
194Mus musculusGene Names: H2-Aa
Find proteins for P04228 (Mus musculus)
Go to UniProtKB:  P04228
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS II I-AD
B
222Mus musculusGene Names: H2-Ab1
Find proteins for P01921 (Mus musculus)
Go to UniProtKB:  P01921
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.255 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.300α = 90.00
b = 101.300β = 90.00
c = 92.600γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance