1F3J

HISTOCOMPATIBILITY ANTIGEN I-AG7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural basis of peptide binding and presentation by the type I diabetes-associated MHC class II molecule of NOD mice.

Latek, R.R.Suri, A.Petzold, S.J.Nelson, C.A.Kanagawa, O.Unanue, E.R.Fremont, D.H.

(2000) Immunity 12: 699-710


  • PubMed Abstract: 
  • We have determined the crystal structure of I-Ag7, an integral component in murine type I diabetes development. Several features distinguish I-Ag7 from other non-autoimmune-associated MHC class II molecules, including novel peptide and heterodimer pa ...

    We have determined the crystal structure of I-Ag7, an integral component in murine type I diabetes development. Several features distinguish I-Ag7 from other non-autoimmune-associated MHC class II molecules, including novel peptide and heterodimer pairing interactions. The binding groove of I-Ag7 is unusual at both terminal ends, with a potentially solvent-exposed channel at the base of the P1 pocket and a widened entrance to the P9 pocket. Peptide binding studies with variants of the hen egg lysozyme I-Ag7 epitope HEL(11-25) support a comprehensive structure-based I-Ag7 binding motif. Residues critical for T cell recognition were investigated with a panel of HEL(11-25)-restricted clones, which uncovered P1 anchor-dependent structural variations. These results establish a framework for future experiments directed at understanding the role of I-Ag7 in autoimmunity.


    Organizational Affiliation

    Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN
A, D
182Mus musculusGene Names: H2-Aa
Find proteins for P04228 (Mus musculus)
Go to UniProtKB:  P04228
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS II NOD
B, E
187Mus musculusGene Names: H2-Ab1
Find proteins for Q31135 (Mus musculus)
Go to UniProtKB:  Q31135
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME C
P, Q
14Gallus gallusGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.221 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 109.540α = 90.00
b = 109.540β = 90.00
c = 176.360γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALAdata scaling
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
CCP4data reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    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
  • Version 1.4: 2017-10-04
    Type: Refinement description