1UVQ

Crystal structure of HLA-DQ0602 in complex with a hypocretin peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Hla-Dq0602 that Protects Against Type 1 Diabetes and Confers Strong Susceptibility to Narcolepsy

Siebold, C.Hansen, B.E.Wyer, J.R.Harlos, K.Esnouf, R.E.Svejgaard, A.Bell, J.I.Strominger, J.L.Jones, E.Y.Fugger, L.

(2004) Proc Natl Acad Sci U S A 101: 1999

  • DOI: 10.1073/pnas.0308458100
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The MHC class II molecule DQ0602 confers strong susceptibility to narcolepsy but dominant protection against type 1 diabetes. The crystal structure of DQ0602 reveals the molecular features underlying these contrasting genetic properties. Structural c ...

    The MHC class II molecule DQ0602 confers strong susceptibility to narcolepsy but dominant protection against type 1 diabetes. The crystal structure of DQ0602 reveals the molecular features underlying these contrasting genetic properties. Structural comparisons to homologous DQ molecules with differential disease associations highlight a previously unrecognized interplay between the volume of the P6 pocket and the specificity of the P9 pocket, which implies that presentation of an expanded peptide repertoire is critical for dominant protection against type 1 diabetes. In narcolepsy, the volume of the P4 pocket appears central to the susceptibility, suggesting that the presentation of a specific peptide population plays a major role.


    Organizational Affiliation

    Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN
A
197Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
Find proteins for E9PMV2 (Homo sapiens)
Go to UniProtKB:  E9PMV2
NIH Common Fund Data Resources

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN
B
198Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1HLA-DQB
Find proteins for P01920 (Homo sapiens)
Go to UniProtKB:  P01920
NIH Common Fund Data Resources
PHAROS  P01920

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
OREXIN
C
33Homo sapiensMutation(s): 0 
Gene Names: HCRTOXPPORXPPOX
Find proteins for O43612 (Homo sapiens)
Go to UniProtKB:  O43612
NIH Common Fund Data Resources
PHAROS  O43612
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
FUC
Query on FUC

Download CCD File 
B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GLY
Query on GLY

Download CCD File 
A
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

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B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.078α = 90
b = 129.304β = 90
c = 40.619γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-05
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance