5VL7

PCSK9 complex with Fab33


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Discovery of a cryptic peptide-binding site on PCSK9 and design of antagonists.

Zhang, Y.Ultsch, M.Skelton, N.J.Burdick, D.J.Beresini, M.H.Li, W.Kong-Beltran, M.Peterson, A.Quinn, J.Chiu, C.Wu, Y.Shia, S.Moran, P.Di Lello, P.Eigenbrot, C.Kirchhofer, D.

(2017) Nat. Struct. Mol. Biol. 24: 848-856

  • DOI: 10.1038/nsmb.3453
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proprotein convertase subtilisin/kexin type 9 (PCSK9) regulates plasma LDL cholesterol (LDL-c) levels by promoting the degradation of liver LDL receptors (LDLRs). Antibodies that inhibit PCSK9 binding to the EGF(A) domain of the LDLR are effective in ...

    Proprotein convertase subtilisin/kexin type 9 (PCSK9) regulates plasma LDL cholesterol (LDL-c) levels by promoting the degradation of liver LDL receptors (LDLRs). Antibodies that inhibit PCSK9 binding to the EGF(A) domain of the LDLR are effective in lowering LDL-c. However, the discovery of small-molecule therapeutics is hampered by difficulty in targeting the relatively flat EGF(A)-binding site on PCSK9. Here we demonstrate that it is possible to target this site, based on the finding that the PCSK9 P' helix displays conformational flexibility. As a consequence, the vacated N-terminal groove of PCSK9, which is adjacent to the EGF(A)-binding site, is in fact accessible to small peptides. In phage-display experiments, the EGF(A)-mimicking peptide Pep2-8 was used as an anchor peptide for the attachment of an extension peptide library directed toward the groove site. Guided by structural information, we further engineered the identified groove-binding peptides into antagonists, which encroach on the EGF(A)-binding site and inhibit LDLR binding.


    Organizational Affiliation

    Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proprotein convertase subtilisin/kexin type 9
A
152Homo 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
548Homo 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
Fab33 heavy chain
H
228N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fab33 light chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.199 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.283α = 90.00
b = 142.523β = 90.00
c = 253.983γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (United States)United StatesDE-AC02-05CH11231
Department of Energy (United States)United StatesDE-AC02-06CH11357
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41GM103393

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence
  • Version 1.3: 2017-10-18
    Type: Database references