› 6dfx

X-ray diffraction
2.03Å resolution

human diabetogenic TCR T1D3 in complex with DQ8-p8E9E peptide

Released:
DOI: 10.2210/pdb6dfx/pdb
PDB entry 6dfx coloured by chain, front view.
PDB entry 6dfx coloured by chain, side view.
PDB entry 6dfx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
How C-terminal additions to insulin B-chain fragments create superagonists for T cells in mouse and human type 1 diabetes.
Wang Y, Sosinowski T, Novikov A, Crawford F, White J, Jin N, Liu Z, Zou J, Neau D, Davidson HW, Nakayama M, Kwok WW, Gapin L, Marrack P, Kappler JW, Dai S
Sci Immunol 4 (2019)
PMID: 30952805

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212219 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
Ig-like domain-containing protein Chains: A, D
Molecule details ›
Chains: A, D
Length: 188 amino acids
Theoretical weight: 21.37 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q30069 (Residues: 3-184; Coverage: 80%)
Gene name: HLA-DQA1
Sequence domains:
Structure domains:
Ig-like domain-containing protein Chains: B, E
Molecule details ›
Chains: B, E
Length: 221 amino acids
Theoretical weight: 25.12 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: U3PYM0 (Residues: 35-223; Coverage: 83%)
Gene name: HLA-DQB1
Sequence domains:
T1D3 alpha chain Chains: G, I
Molecule details ›
Chains: G, I
Length: 207 amino acids
Theoretical weight: 22.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
Structure domains: Immunoglobulins
T1D3 beta chain Chains: H, J
Molecule details ›
Chains: H, J
Length: 238 amino acids
Theoretical weight: 26.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
Structure domains: Immunoglobulins

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 111.705Å b: 88.896Å c: 116.777Å
α: 90° β: 104.26° γ: 90°
R-values:
R R work R free
0.183 0.181 0.217
Expression systems:
  • Trichoplusia ni
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

8 review citations

Peptide mimotopes alter T cell function in cancer and autoimmunity.
Slansky et al. (2020)
7 more

6 mentions without citation

The Many Faces of CD4+ T Cells: Immunological and Structural Characteristics.
Chatzileontiadou et al. (2020)
5 more