› 4wdi

X-ray diffraction
2.31Å resolution

Weak TCR binding to an unstable insulin epitope drives type 1 diabetes

Released:
DOI: 10.2210/pdb4wdi/pdb
PDB entry 4wdi coloured by chain, front view.
PDB entry 4wdi coloured by chain, side view.
PDB entry 4wdi coloured by chain, top view.
Source organisms:
Primary publication:
Distortion of the Major Histocompatibility Complex Class I Binding Groove to Accommodate an Insulin-derived 10-Mer Peptide.
Motozono C, Pearson JA, De Leenheer E, Rizkallah PJ, Beck K, Trimby A, Sewell AK, Wong FS, Cole DK
J Biol Chem 290 18924-33 (2015)
PMID: 26085090

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-134197 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
H-2 class I histocompatibility antigen, K-D alpha chain Chains: A, D
Molecule details ›
Chains: A, D
Length: 277 amino acids
Theoretical weight: 32.35 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01902 (Residues: 22-296; Coverage: 79%)
Gene names: H2-K, H2-K1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, E
Molecule details ›
Chains: B, E
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Insulin B chain Chains: C, F
Molecule details ›
Chains: C, F
Length: 9 amino acids
Theoretical weight: 1.01 KDa
Source organism: Homo sapiens
Expression system: synthetic construct
UniProt:
  • Canonical: P01308 (Residues: 39-47; Coverage: 11%)
Gene name: INS

Ligands and Environments

2 bound ligands:
Ligand EDO 1 x EDO
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P1
Unit cell:
a: 46.93Å b: 62.69Å c: 72.67Å
α: 68.11° β: 85.79° γ: 85.18°
R-values:
R R work R free
0.21 0.206 0.283
Expression systems:
  • Escherichia coli BL21(DE3)
  • synthetic construct

Quick links

Citations

4 review citations

Unfinished Business: Evolution of the MHC and the Adaptive Immune System of Jawed Vertebrates.
Kaufman J. (2018)
3 more

1 mention without citation

Distortion of the Major Histocompatibility Complex Class I Binding Groove to Accommodate an Insulin-derived 10-Mer Peptide.
Motozono et al. (2015)