› 3p5b

X-ray diffraction
3.3Å resolution

The structure of the LDLR/PCSK9 complex reveals the receptor in an extended conformation

Released:
DOI: 10.2210/pdb3p5b/pdb
PDB entry 3p5b coloured by chain, front view.
PDB entry 3p5b coloured by chain, side view.
PDB entry 3p5b coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanistic implications for LDL receptor degradation from the PCSK9/LDLR structure at neutral pH.
Lo Surdo P, Bottomley MJ, Calzetta A, Settembre EC, Cirillo A, Pandit S, Ni YG, Hubbard B, Sitlani A, Carfí A
EMBO Rep 12 1300-5 (2011)
PMID: 22081141

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-134047 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Proprotein convertase subtilisin/kexin type 9 Chain: P
Molecule details ›
Chain: P
Length: 92 amino acids
Theoretical weight: 10.49 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8NBP7 (Residues: 61-152; Coverage: 14%)
Gene names: NARC1, PCSK9, PSEC0052
Sequence domains: Peptidase inhibitor I9
Structure domains: Peptidase S8 propeptide/proteinase inhibitor I9
Proprotein convertase subtilisin/kexin type 9 Chain: A
Molecule details ›
Chain: A
Length: 540 amino acids
Theoretical weight: 57.37 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8NBP7 (Residues: 153-692; Coverage: 82%)
Gene names: NARC1, PCSK9, PSEC0052
Sequence domains:
Structure domains:
Low-density lipoprotein receptor Chain: L
Molecule details ›
Chain: L
Length: 400 amino acids
Theoretical weight: 44.76 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P01130 (Residues: 316-715; Coverage: 48%)
Gene name: LDLR
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand CA 3 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P212121
Unit cell:
a: 77Å b: 109.701Å c: 178.456Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.275 0.271 0.298
Expression system: Homo sapiens

Quick links

Citations

48 review citations

The biology and therapeutic targeting of the proprotein convertases.
Seidah et al. (2012)
47 more

11 mentions without citation

PCSK9 as a Target for Development of a New Generation of Hypolipidemic Drugs.
Kuzmich et al. (2022)
10 more