ISDA

Deposition Date 2010-10-08

Release Date 2011-10-26

Last Version Date 2024-11-20

Entry Detail

PDB ID:

3P5B

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:

3.30 Å

R-Value Free:

0.29

R-Value Work:

0.27

R-Value Observed:

0.27

Space Group:

P 21 21 21

Download 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:400
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P01130 Pfam ID: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

Primary Citation

Mechanistic implications for LDL receptor degradation from the PCSK9/LDLR structure at neutral pH.

Lo Surdo, P, Bottomley, M.J, Calzetta, A, Settembre, E.C, Cirillo, A, Pandit, S, Ni, Y.G, Hubbard, B, Sitlani, A, Carfi, A.Show

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