6DIG

Crystal structure of DQA1*01:02/DQB1*06:02 in complex with a hypocretin peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

In vivo clonal expansion and phenotypes of hypocretin-specific CD4+T cells in narcolepsy patients and controls.

Jiang, W.Birtley, J.R.Hung, S.C.Wang, W.Chiou, S.H.Macaubas, C.Kornum, B.Tian, L.Huang, H.Adler, L.Weaver, G.Lu, L.Ilstad-Minnihan, A.Somasundaram, S.Ayyangar, S.Davis, M.M.Stern, L.J.Mellins, E.D.

(2019) Nat Commun 10: 5247-5247

  • DOI: https://doi.org/10.1038/s41467-019-13234-x
  • Primary Citation of Related Structures:  
    6DIG

  • PubMed Abstract: 

    Individuals with narcolepsy suffer from abnormal sleep patterns due to loss of neurons that uniquely supply hypocretin (HCRT). Previous studies found associations of narcolepsy with the human leukocyte antigen (HLA)-DQ6 allele and T-cell receptor α (TRA) J24 gene segment and also suggested that in vitro-stimulated T cells can target HCRT. Here, we present evidence of in vivo expansion of DQ6-HCRT tetramer + /TRAJ24 + /CD4 + T cells in DQ6 + individuals with and without narcolepsy. We identify related TRAJ24 + TCRαβ clonotypes encoded by identical α/β gene regions from two patients and two controls. TRAJ24-G allele + clonotypes only expand in the two patients, whereas a TRAJ24-C allele + clonotype expands in a control. A representative tetramer + /G-allele + TCR shows signaling reactivity to the epitope HCRT 87-97 . Clonally expanded G-allele + T cells exhibit an unconventional effector phenotype. Our analysis of in vivo expansion of HCRT-reactive TRAJ24 + cells opens an avenue for further investigation of the autoimmune contribution to narcolepsy development.


  • Organizational Affiliation

    Department of Pediatrics-Human Gene Therapy, Stanford University School of medicine, Stanford, CA, 94305, USA. wjiang6@stanford.edu.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class II HLA-DQ-alpha chain207Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
UniProt
Find proteins for Q30066 (Homo sapiens)
Explore Q30066 
Go to UniProtKB:  Q30066
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ30066
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DQ beta 1 chain215Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SU54 (Homo sapiens)
Explore Q5SU54 
Go to UniProtKB:  Q5SU54
GTEx:  ENSG00000179344 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SU54
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
13-mer peptide: ALA-GLY-ASN-HIS-ALA-ALA-GLY-ILE-LEU-THR-LEU-GLY-LYS13Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.666α = 90
b = 89.596β = 99.517
c = 90.928γ = 90
Software Package:
Software NamePurpose
phenix.refinerefinement
PHENIXrefinement
xia2data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States5 U01 AI101990

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references, Structure summary
  • Version 1.2: 2019-12-04
    Changes: Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary