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 

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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: https://doi.org/10.1073/pnas.0308458100
  • Primary Citation of Related Structures:  
    1UVQ

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN197Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for E9PMV2 (Homo sapiens)
Explore E9PMV2 
Go to UniProtKB:  E9PMV2
GTEx:  ENSG00000196735 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9PMV2
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN198Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01920 (Homo sapiens)
Explore P01920 
Go to UniProtKB:  P01920
PHAROS:  P01920
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01920
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01920-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
OREXIN33Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O43612 (Homo sapiens)
Explore O43612 
Go to UniProtKB:  O43612
PHAROS:  O43612
GTEx:  ENSG00000161610 
Entity Groups  
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UniProt GroupO43612
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
D
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Small Molecules
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary