1IAO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


This is version 1.4 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

  • DOI: https://doi.org/10.1016/s1074-7613(00)80537-3
  • Primary Citation of Related Structures:  
    1IAO, 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC CLASS II I-AD194Mus musculusMutation(s): 0 
UniProt
Find proteins for P04228 (Mus musculus)
Explore P04228 
Go to UniProtKB:  P04228
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04228
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MHC CLASS II I-AD222Mus musculusMutation(s): 0 
UniProt
Find proteins for P01921 (Mus musculus)
Explore P01921 
Go to UniProtKB:  P01921
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01921
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.3α = 90
b = 101.3β = 90
c = 92.6γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-11-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-08-09
    Changes: Database references, Refinement description, Structure summary