5OCA

PCSK9:Fab Complex with Dextran Sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Heparan sulfate proteoglycans present PCSK9 to the LDL receptor.

Gustafsen, C.Olsen, D.Vilstrup, J.Lund, S.Reinhardt, A.Wellner, N.Larsen, T.Andersen, C.B.F.Weyer, K.Li, J.P.Seeberger, P.H.Thirup, S.Madsen, P.Glerup, S.

(2017) Nat Commun 8: 503-503

  • DOI: 10.1038/s41467-017-00568-7

  • PubMed Abstract: 
  • Coronary artery disease is the main cause of death worldwide and accelerated by increased plasma levels of cholesterol-rich low-density lipoprotein particles (LDL). Circulating PCSK9 contributes to coronary artery disease by inducing lysosomal degrad ...

    Coronary artery disease is the main cause of death worldwide and accelerated by increased plasma levels of cholesterol-rich low-density lipoprotein particles (LDL). Circulating PCSK9 contributes to coronary artery disease by inducing lysosomal degradation of the LDL receptor (LDLR) in the liver and thereby reducing LDL clearance. Here, we show that liver heparan sulfate proteoglycans are PCSK9 receptors and essential for PCSK9-induced LDLR degradation. The heparan sulfate-binding site is located in the PCSK9 prodomain and formed by surface-exposed basic residues interacting with trisulfated heparan sulfate disaccharide repeats. Accordingly, heparan sulfate mimetics and monoclonal antibodies directed against the heparan sulfate-binding site are potent PCSK9 inhibitors. We propose that heparan sulfate proteoglycans lining the hepatocyte surface capture PCSK9 and facilitates subsequent PCSK9:LDLR complex formation. Our findings provide new insights into LDL biology and show that targeting PCSK9 using heparan sulfate mimetics is a potential therapeutic strategy in coronary artery disease.PCSK9 interacts with LDL receptor, causing its degradation, and consequently reduces the clearance of LDL. Here, Gustafsen et al. show that PCSK9 interacts with heparan sulfate proteoglycans and this binding favors LDLR degradation. Pharmacological inhibition of this binding can be exploited as therapeutic intervention to lower LDL levels.


    Organizational Affiliation

    Scienion AG, Volmerstrasse 7b, 12489, Berlin, Germany.,Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark.,Department of Biomedicine, Aarhus University, Ole Worms Allé 3, 8000, Aarhus, Denmark. gustafsen@biomed.au.dk.,Department of Medical Biochemistry and Microbiology, University of Uppsala, Husarg. 3, 75237, Uppsala, Sweden.,Department of Biomedicine, Aarhus University, Ole Worms Allé 3, 8000, Aarhus, Denmark. glerup@biomed.au.dk.,Department of Animal Science, Aarhus University, Blichers Allé 20, 8830, Tjele, Denmark.,Department of Biomolecular Systems, Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1 OT Golm, 14476, Potsdam, Germany.,Department of Biomedicine, Aarhus University, Ole Worms Allé 3, 8000, Aarhus, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proprotein convertase subtilisin/kexin type 9
A
126Homo sapiensMutation(s): 0 
Gene Names: PCSK9 (NARC1)
EC: 3.4.21.-
Find proteins for Q8NBP7 (Homo sapiens)
Go to Gene View: PCSK9
Go to UniProtKB:  Q8NBP7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proprotein convertase subtilisin/kexin type 9
B
540Homo sapiensMutation(s): 0 
Gene Names: PCSK9 (NARC1)
EC: 3.4.21.-
Find proteins for Q8NBP7 (Homo sapiens)
Go to Gene View: PCSK9
Go to UniProtKB:  Q8NBP7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab from LDLR competitive antibody: Heavy chain
H
238N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fab from LDLR competitive antibody: Light chain
L
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
9QZ
Query on 9QZ

Download SDF File 
Download CCD File 
A
[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-[[(2~{S},3~{S},4~{R},5~{S},6~{R})-3,6-bis(oxidanyl)-4,5-disulfooxy-oxan-2-yl]methoxy]-6-(hydroxymethyl)-3,5-disulfooxy-oxan-4-yl] hydrogen sulfate
C12 H22 O26 S5
SNMGREPYXWHBJB-FDEZJODUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9QZKd: 180000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 264.721α = 90.00
b = 137.352β = 102.84
c = 69.885γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2019-10-16
    Type: Data collection