1IAK

HISTOCOMPATIBILITY ANTIGEN I-AK

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure of I-Ak in complex with a dominant epitope of lysozyme.

Fremont, D.H., Monnaie, D., Nelson, C.A., Hendrickson, W.A., Unanue, E.R.

(1998) Immunity 8: 305-317


  • PubMed Abstract: 

    • We have determined the structure of murine MHC class II I-Ak in complex with a naturally processed peptide from hen egg lysozyme (HEL residues 50-62) at 1.9 A resolution. These results provide a structural basis for the I-Ak peptide-binding motif. Bi ...

    We have determined the structure of murine MHC class II I-Ak in complex with a naturally processed peptide from hen egg lysozyme (HEL residues 50-62) at 1.9 A resolution. These results provide a structural basis for the I-Ak peptide-binding motif. Binding is established by the deep burial of five anchor side chains into specific pockets of the I-Ak binding groove, with a zen-like fit of an aspartic acid in the P1 pocket. We also show that in the I-Ak alpha chain, a bulge occurs in the first strand of the peptide-binding platform, an insertion probably common to all I-A and HLA-DQ alleles. The I-Ak beta chain has a deletion in the helical region adjacent to the P7 pocket and an insertion in the helical region neighboring the P1 pocket. As a result of these structural features, the extended HEL peptide dips low into the center of the I-Ak groove and reaches toward solvent at its C-terminal end.

    Organizational Affiliation: 

    Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA. fremont@immunology.wustl.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS II I-AK
A
199Mus musculusGene Names: H2-Aa
Find proteins for P01910 (Mus musculus)
Go to UniProtKB:  P01910
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS II I-AK
B
185Mus musculusGene Names: H2-Ab1
Find proteins for P06343 (Mus musculus)
Go to UniProtKB:  P06343
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS II I-AK
P
13Ovis aries
Find proteins for Q29431 (Ovis aries)
Go to UniProtKB:  Q29431
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.214 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 112.250α = 90.00
b = 112.250β = 90.00
c = 99.720γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
AGROVATAdata reduction
X-PLORphasing
HKLdata reduction
SCALAdata scaling
X-PLORmodel building
HKLdata collection
DENZOdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model