5OCA

PCSK9:Fab Complex with Dextran Sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 2.1 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: https://doi.org/10.1038/s41467-017-00568-7
  • Primary Citation of Related Structures:  
    5OCA

  • 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 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

    Department of Biomedicine, Aarhus University, Ole Worms Allé 3, 8000, Aarhus, Denmark. gustafsen@biomed.au.dk.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proprotein convertase subtilisin/kexin type 9126Homo sapiensMutation(s): 0 
Gene Names: PCSK9NARC1PSEC0052
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBP7 (Homo sapiens)
Explore Q8NBP7 
Go to UniProtKB:  Q8NBP7
PHAROS:  Q8NBP7
GTEx:  ENSG00000169174 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NBP7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proprotein convertase subtilisin/kexin type 9540Homo sapiensMutation(s): 0 
Gene Names: PCSK9NARC1PSEC0052
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBP7 (Homo sapiens)
Explore Q8NBP7 
Go to UniProtKB:  Q8NBP7
PHAROS:  Q8NBP7
GTEx:  ENSG00000169174 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NBP7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab from LDLR competitive antibody: Heavy chainC [auth H]238Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab from LDLR competitive antibody: Light chainD [auth L]217Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2,3,4-tri-O-sulfo-beta-D-altropyranose-(1-6)-2,3-di-O-sulfo-alpha-L-glucopyranoseE [auth C]2N/A
Glycosylation Resources
GlyTouCan:  G96300CN
GlyCosmos:  G96300CN
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 264.721α = 90
b = 137.352β = 102.84
c = 69.885γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-11-06
    Changes: Data collection, Database references, Structure summary