› 5wob

X-ray diffraction
3.95Å resolution

Crystal Structure Analysis of Fab1-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Insulin

Released:
DOI: 10.2210/pdb5wob/pdb
PDB entry 5wob coloured by chain, front view.
PDB entry 5wob coloured by chain, side view.
PDB entry 5wob coloured by chain, top view.
Source organisms:
Primary publication:
Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme.
Zhang Z, Liang WG, Bailey LJ, Tan YZ, Wei H, Wang A, Farcasanu M, Woods VA, McCord LA, Lee D, Shang W, Deprez-Poulain R, Deprez B, Liu DR, Koide A, Koide S, Kossiakoff AA, Li S, Carragher B, Potter CS, Tang WJ
Elife 7 (2018)
PMID: 29596046

Function and Biology Details

Reaction catalysed: 
Degradation of insulin, glucagon and other polypeptides. No action on proteins.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-230722 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Insulin-degrading enzyme Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 990 amino acids
Theoretical weight: 114.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P14735 (Residues: 42-1019; Coverage: 96%)
Gene name: IDE
Sequence domains:
Structure domains: Metalloenzyme, LuxS/M16 peptidase-like
Insulin A chain Chains: a, b, c, d, e, f, g, h
Molecule details ›
Chains: a, b, c, d, e, f, g, h
Length: 20 amino acids
Theoretical weight: 2.27 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P01308 (Residues: 90-109; Coverage: 23%)
Gene name: INS
IDE-bound Fab heavy chain Chains: I, K, M, O, Q, S, U, W
Molecule details ›
Chains: I, K, M, O, Q, S, U, W
Length: 263 amino acids
Theoretical weight: 28.2 KDa
Source organism: Mus musculoides
Expression system: Escherichia coli
Structure domains: Immunoglobulins
IDE-bound Fab light chain Chains: J, L, N, P, R, T, V, X
Molecule details ›
Chains: J, L, N, P, R, T, V, X
Length: 239 amino acids
Theoretical weight: 25.98 KDa
Source organism: Mus musculoides
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 121.589Å b: 138.19Å c: 376.509Å
α: 90° β: 99.36° γ: 90°
R-values:
R R work R free
0.244 0.243 0.291
Expression systems:
  • Escherichia coli
  • Saccharomyces cerevisiae

Quick links

Citations

7 review citations

Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.
Brosey et al. (2019)
6 more

1 mention without citation

Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme.
Zhang et al. (2018)