2W2O

PCSK9-deltaC D374Y mutant bound to WT EGF-A of LDLR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Biochemical Characterization of the Wild Type Pcsk9/Egf-Ab Complex and Natural Fh Mutants.

Bottomley, M.J.Cirillo, A.Orsatti, L.Ruggeri, L.Fisher, T.S.Santoro, J.C.Cummings, R.T.Cubbon, R.M.Lo Surdo, P.Calzetta, A.Noto, A.Baysarowich, J.Mattu, M.Talamo, F.De Francesco, R.Sparrow, C.P.Sitlani, A.Carfi, A.

(2009) J.Biol.Chem. 284: 1313

  • DOI: 10.1074/jbc.M808363200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PCSK9 regulates low density lipoprotein receptor (LDLR) levels and consequently is a target for the prevention of atherosclerosis and coronary heart disease. Here we studied the interaction, of LDLR EGF(A/AB) repeats with PCSK9. We show that PCSK9 bi ...

    PCSK9 regulates low density lipoprotein receptor (LDLR) levels and consequently is a target for the prevention of atherosclerosis and coronary heart disease. Here we studied the interaction, of LDLR EGF(A/AB) repeats with PCSK9. We show that PCSK9 binds the EGF(AB) repeats in a pH-dependent manner. Although the PCSK9 C-terminal domain is not involved in LDLR binding, PCSK9 autocleavage is required. Moreover, we report the x-ray structure of the PCSK9DeltaC-EGF(AB) complex at neutral pH. Compared with the low pH PCSK9-EGF(A) structure, the new structure revealed rearrangement of the EGF(A) His-306 side chain and disruption of the salt bridge with PCSK9 Asp-374, thus suggesting the basis for enhanced interaction at low pH. In addition, the structure of PCSK9DeltaC bound to EGF(AB)(H306Y), a mutant associated with familial hypercholesterolemia (FH), reveals that the Tyr-306 side chain forms a hydrogen bond with PCSK9 Asp-374, thus mimicking His-306 in the low pH conformation. Consistently, Tyr-306 confers increased affinity for PCSK9. Importantly, we found that although the EGF(AB)(H306Y)-PCSK9 interaction is pH-independent, LDLR(H306Y) binds PCSK9 50-fold better at low pH, suggesting that factors other than His-306 contribute to the pH dependence of PCSK9-LDLR binding. Further, we determined the structures of EGF(AB) bound to PCSK9DeltaC containing the FH-associated D374Y and D374H mutations, revealing additional interactions with EGF(A) mediated by Tyr-374/His-374 and providing a rationale for their disease phenotypes. Finally, we report the inhibitory properties of EGF repeats in a cellular assay measuring LDL uptake.


    Organizational Affiliation

    Department of Biochemistry, Istituto di Ricerca di Biologia Molecolare "P. Angeletti", Via Pontina Km 30.600, 00040 Pomezia (Rome), Italy. matthew_bottomley@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
A
312Homo sapiensMutation(s): 1 
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
LOW-DENSITY LIPOPROTEIN RECEPTOR
E
107Homo sapiensMutation(s): 0 
Gene Names: LDLR
Find proteins for P01130 (Homo sapiens)
Go to Gene View: LDLR
Go to UniProtKB:  P01130
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
P
114Homo 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
CA
Query on CA

Download SDF File 
Download CCD File 
E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.227 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 85.948α = 90.00
b = 85.948β = 90.00
c = 218.329γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2008-11-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance