› 4nge

X-ray diffraction
2.7Å resolution

Crystal Structure of Human Presequence Protease in Complex with Amyloid-beta (1-40)

Released:
DOI: 10.2210/pdb4nge/pdb
PDB entry 4nge coloured by chain, front view.
PDB entry 4nge coloured by chain, side view.
PDB entry 4nge coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis of substrate recognition and degradation by human presequence protease.
King JV, Liang WG, Scherpelz KP, Schilling AB, Meredith SC, Tang WJ
Structure 22 996-1007 (2014)
PMID: 24931469

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-138367 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Presequence protease, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 1014 amino acids
Theoretical weight: 115.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5JRX3 (Residues: 33-1037; Coverage: 97%)
Gene names: KIAA1104, MP1, PITRM1, PREP
Sequence domains:
Structure domains: Metalloenzyme, LuxS/M16 peptidase-like
Amyloid-beta protein 40 Chains: B, E
Molecule details ›
Chains: B, E
Length: 40 amino acids
Theoretical weight: 4.34 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P05067 (Residues: 672-711; Coverage: 5%)
Gene names: A4, AD1, APP
Sequence domains: Beta-amyloid peptide (beta-APP)
Beta-amyloid protein 40 Chains: C, F
Molecule details ›
Chains: C, F
Length: 7 amino acids
Theoretical weight: 614 Da
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
Presequence protease, mitochondrial Chain: D
Molecule details ›
Chain: D
Length: 1014 amino acids
Theoretical weight: 115.57 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q5JRX3 (Residues: 33-1037; Coverage: 97%)
Gene names: KIAA1104, MP1, PITRM1, PREP
Sequence domains:
Structure domains: Metalloenzyme, LuxS/M16 peptidase-like

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand GOL 3 x GOL
Ligand ACT 2 x ACT
3 modified residues:
Ligand CAS 5 x CAS
Ligand MLY 37 x MLY
Ligand MLZ 1 x MLZ

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2
Unit cell:
a: 247.275Å b: 86.183Å c: 158.611Å
α: 90° β: 127.56° γ: 90°
R-values:
R R work R free
0.193 0.191 0.232
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

β-Amyloid: the key peptide in the pathogenesis of Alzheimer's disease.
Sun et al. (2015)
3 more

3 mentions without citation

Molecular basis of substrate recognition and degradation by human presequence protease.
King et al. (2014)
2 more