› 6dig

X-ray diffraction
2Å resolution

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

Released:
DOI: 10.2210/pdb6dig/pdb
PDB entry 6dig coloured by chain, front view.
PDB entry 6dig coloured by chain, side view.
PDB entry 6dig coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
In vivo clonal expansion and phenotypes of hypocretin-specific CD4+ T cells in narcolepsy patients and controls.
Jiang W, Birtley JR, Hung SC, Wang W, Chiou SH, Macaubas C, Kornum B, Tian L, Huang H, Adler L, Weaver G, Lu L, Ilstad-Minnihan A, Somasundaram S, Ayyangar S, Davis MM, Stern LJ, Mellins ED
Nat Commun 10 5247 (2019)
PMID: 31748512

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-166590 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 207 amino acids
Theoretical weight: 23.21 KDa
Source organism: Homo sapiens
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: Q30066 (Residues: 1-196; Coverage: 86%)
Gene name: HLA-DQA1
Sequence domains:
Structure domains:
Ig-like domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 215 amino acids
Theoretical weight: 24.39 KDa
Source organism: Homo sapiens
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: Q5SU54 (Residues: 35-230; Coverage: 82%)
Gene name: HLA-DQB1
Sequence domains:
13-mer peptide: ALA-GLY-ASN-HIS-ALA-ALA-GLY-ILE-LEU-THR-LEU-GLY-LYS Chain: C
Molecule details ›
Chain: C
Length: 13 amino acids
Theoretical weight: 1.22 KDa
Source organism: Homo sapiens
Expression system: Drosophila melanogaster

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 2 x NAG
Ligand TRS 1 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: C2
Unit cell:
a: 63.666Å b: 89.596Å c: 90.928Å
α: 90° β: 99.517° γ: 90°
R-values:
R R work R free
0.218 0.216 0.255
Expression system: Drosophila melanogaster

Quick links

Citations

10 review citations

Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors.
Lee et al. (2020)
9 more

7 mentions without citation

In vivo clonal expansion and phenotypes of hypocretin-specific CD4+ T cells in narcolepsy patients and controls.
Jiang et al. (2019)
6 more