1ES0 | pdb_00001es0

CRYSTAL STRUCTURE OF THE MURINE CLASS II ALLELE I-A(G7) COMPLEXED WITH THE GLUTAMIC ACID DECARBOXYLASE (GAD65) PEPTIDE 207-220


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

A structural framework for deciphering the link between I-Ag7 and autoimmune diabetes.

Corper, A.L.Stratmann, T.Apostolopoulos, V.Scott, C.A.Garcia, K.C.Kang, A.S.Wilson, I.A.Teyton, L.

(2000) Science 288: 505-511

  • DOI: https://doi.org/10.1126/science.288.5465.505
  • Primary Citation of Related Structures:  
    1ES0

  • PubMed Abstract: 

    Susceptibility to murine and human insulin-dependent diabetes mellitus correlates strongly with major histocompatibility complex (MHC) class II I-A or HLA-DQ alleles that lack an aspartic acid at position beta57. I-Ag7 lacks this aspartate and is the only class II allele expressed by the nonobese diabetic mouse. The crystal structure of I-Ag7 was determined at 2.6 angstrom resolution as a complex with a high-affinity peptide from the autoantigen glutamic acid decarboxylase (GAD) 65. I-Ag7 has a substantially wider peptide-binding groove around beta57, which accounts for distinct peptide preferences compared with other MHC class II alleles. Loss of Asp(beta57) leads to an oxyanion hole in I-Ag7 that can be filled by peptide carboxyl residues or, perhaps, through interaction with the T cell receptor.


  • Organizational Affiliation
    • Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN190Mus 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
65 KD GLUTAMIC ACID DECARBOXYLASE+H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN221Homo sapiensMutation(s): 0 
EC: 4.1.1.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q05329 (Homo sapiens)
Explore Q05329 
Go to UniProtKB:  Q05329
PHAROS:  Q05329
GTEx:  ENSG00000136750 
Find proteins for Q31135 (Mus musculus)
Explore Q31135 
Go to UniProtKB:  Q31135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ31135Q05329
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.149α = 90
b = 110.123β = 90
c = 96.084γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-28
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2023-08-09
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-10-09
    Changes: Structure summary