3P5C image
Deposition Date 2010-10-08
Release Date 2011-10-26
Last Version Date 2024-11-06
Entry Detail
PDB ID:
3P5C
Keywords:
HYDROLASE/LIPID BINDING PROTEIN
Title:
The structure of the LDLR/PCSK9 complex reveals the receptor in an extended conformation
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Homo sapiens
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
4.20 Å
R-Value Free:
0.34
R-Value Work:
0.32
R-Value Observed:
0.32
Space Group:
P 65
3P5C validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proprotein convertase subtilisin/kexin type 9
Gene (Uniprot):PCSK9
Chain IDs:B (auth: A)
Chain Length:540
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8NBP7 Pfam ID:PF00082, PF18459, PF18464, PF18463, PF05922 EC:3.4.21.61
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Low density lipoprotein receptor variant
Chain IDs:C (auth: L)
Chain Length:440
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P01130 Pfam ID:PF00057, PF00058, PF14670
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proprotein convertase subtilisin/kexin type 9
Gene (Uniprot):PCSK9
Chain IDs:A (auth: P)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8NBP7 Pfam ID:PF00082, PF18459, PF18464, PF18463, PF05922 EC:3.4.21.61
Ligand Molecules
CA
Primary Citation
Mechanistic implications for LDL receptor degradation from the PCSK9/LDLR structure at neutral pH.
Embo Rep. 12 1300 1305 (2011)
PMID: 22081141 DOI: 10.1038/embor.2011.205

Abstact

The protein PCSK9 (proprotein convertase subtilisin/kexin type 9) is a key regulator of low-density lipoprotein receptor (LDLR) levels and cardiovascular health. We have determined the crystal structure of LDLR bound to PCSK9 at neutral pH. The structure shows LDLR in a new extended conformation. The PCSK9 C-terminal domain is solvent exposed, enabling cofactor binding, whereas the catalytic domain and prodomain interact with LDLR epidermal growth factor(A) and β-propeller domains, respectively. Thus, PCSK9 seems to hold LDLR in an extended conformation and to interfere with conformational rearrangements required for LDLR recycling.

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Disease

Primary Citation of related structures
3P5B