2P4E

Crystal Structure of PCSK9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and biophysical studies of PCSK9 and its mutants linked to familial hypercholesterolemia.

Cunningham, D.Danley, D.E.Geoghegan, K.F.Griffor, M.C.Hawkins, J.L.Subashi, T.A.Varghese, A.H.Ammirati, M.J.Culp, J.S.Hoth, L.R.Mansour, M.N.McGrath, K.M.Seddon, A.P.Shenolikar, S.Stutzman-Engwall, K.J.Warren, L.C.Xia, D.Qiu, X.

(2007) Nat.Struct.Mol.Biol. 14: 413-419

  • DOI: 10.1038/nsmb1235

  • PubMed Abstract: 
  • Proprotein convertase subtilisin kexin type 9 (PCSK9) lowers the abundance of surface low-density lipoprotein (LDL) receptor through an undefined mechanism. The structure of human PCSK9 shows the subtilisin-like catalytic site blocked by the prodomai ...

    Proprotein convertase subtilisin kexin type 9 (PCSK9) lowers the abundance of surface low-density lipoprotein (LDL) receptor through an undefined mechanism. The structure of human PCSK9 shows the subtilisin-like catalytic site blocked by the prodomain in a noncovalent complex and inaccessible to exogenous ligands, and that the C-terminal domain has a novel fold. Biosensor studies show that PCSK9 binds the extracellular domain of LDL receptor with K(d) = 170 nM at the neutral pH of plasma, but with a K(d) as low as 1 nM at the acidic pH of endosomes. The D374Y gain-of-function mutant, associated with hypercholesterolemia and early-onset cardiovascular disease, binds the receptor 25 times more tightly than wild-type PCSK9 at neutral pH and remains exclusively in a high-affinity complex at the acidic pH. PCSK9 may diminish LDL receptors by a mechanism that requires direct binding but not necessarily receptor proteolysis.


    Organizational Affiliation

    Pfizer Inc., Eastern Point Road, Groton, Connecticut 06430, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proprotein convertase subtilisin/kexin type 9
P, A
692Homo 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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download SDF File 
Download CCD File 
P
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.810α = 90.00
b = 70.670β = 90.00
c = 150.020γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
AMoREphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance