1JK8

Crystal structure of a human insulin peptide-HLA-DQ8 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a human insulin peptide-HLA-DQ8 complex and susceptibility to type 1 diabetes.

Lee, K.H.Wucherpfennig, K.W.Wiley, D.C.

(2001) Nat.Immunol. 2: 501-507

  • DOI: 10.1038/88694

  • PubMed Abstract: 
  • The class II major histocompatibility complex (MHC) glycoproteins HLA-DQ8 and HLA-DQ2 in humans and I-A(g7) in nonobese diabetic (NOD) mice are the major risk factors for increased susceptibility to type 1 diabetes. Using X-ray crystallography, we ha ...

    The class II major histocompatibility complex (MHC) glycoproteins HLA-DQ8 and HLA-DQ2 in humans and I-A(g7) in nonobese diabetic (NOD) mice are the major risk factors for increased susceptibility to type 1 diabetes. Using X-ray crystallography, we have determined the three-dimensional structure of DQ8 complexed with an immunodominant peptide from insulin. The similarity of the DQ8, DQ2 and I-A(g7) peptide-binding pockets suggests that diabetes is caused by the same antigen-presentation event(s) in humans and NOD mice. Correlating type 1 diabetes epidemiology and MHC sequences with the DQ8 structure suggests that other structural features of the P9 pocket in addition to position 57 contribute to susceptibility to type 1 diabetes.


    Organizational Affiliation

    Laboratory of Molecular Medicine, The Department of Medicine, The Children's Hospital, 320 Longwood Avenue, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC class II HLA-DQ8
A
181Homo sapiensGene Names: HLA-DQA1
Find proteins for P01909 (Homo sapiens)
Go to Gene View: HLA-DQA1
Go to UniProtKB:  P01909
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC class II HLA-DQ8
B
190Homo sapiensGene Names: HLA-DQB1 (HLA-DQB)
Find proteins for P01920 (Homo sapiens)
Go to Gene View: HLA-DQB1
Go to UniProtKB:  P01920
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
insulin B peptide
C
14Homo sapiensGene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to Gene View: INS
Go to UniProtKB:  P01308
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.034α = 90.00
b = 42.862β = 102.48
c = 87.467γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-22
    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: 2018-01-31
    Type: Advisory, Experimental preparation