6MV5

Anti-PCSK9 fab 6E2 bound to the N-terminal peptide from PCSK9 (E32K)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Identification of a Helical Segment within the Intrinsically Disordered Region of the PCSK9 Prodomain.

Ultsch, M.Li, W.Eigenbrot, C.Di Lello, P.Lipari, M.T.Gerhardy, S.AhYoung, A.P.Quinn, J.Franke, Y.Chen, Y.Kong Beltran, M.Peterson, A.Kirchhofer, D.

(2019) J. Mol. Biol. 431: 885-903

  • DOI: 10.1016/j.jmb.2018.11.025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proprotein convertase subtilisin/kexin 9 (PCSK9) is a key regulator of lipid metabolism by degrading liver LDL receptors. Structural studies have provided molecular details of PCSK9 function. However, the N-terminal acidic stretch of the PCSK9 prodom ...

    Proprotein convertase subtilisin/kexin 9 (PCSK9) is a key regulator of lipid metabolism by degrading liver LDL receptors. Structural studies have provided molecular details of PCSK9 function. However, the N-terminal acidic stretch of the PCSK9 prodomain (Q31-T60) has eluded structural investigation, since it is in a disordered state. The interest in this region is intensified by the presence of human missense mutations associated with low and high LDL-c levels (E32K, D35Y, and R46L, respectively), as well as two posttranslationally modified sites, sulfated Y38 and phosphorylated S47. Herein we show that a segment within this region undergoes disorder-to-order transition. Experiments with acidic stretch-derived peptides demonstrated that the folding is centered at the segment Y38-L45, which adopts an α-helix as determined by NMR analysis of free peptides and by X-ray crystallography of peptides in complex with antibody 6E2 (Ab6E2). In the Fab6E2-peptide complexes, the structured region features a central 2 1/4-turn α-helix and encompasses up to 2/3 of the length of the acidic stretch, including the missense mutations and posttranslationally modified sites. Experiments with helix-breaking proline substitutions in peptides and in PCSK9 protein indicated that Ab6E2 specifically recognizes the helical conformation of the acidic stretch. Therefore, the observed quantitative binding of Ab6E2 to native PCSK9 from various cell lines suggests that the disorder-to-order transition is a true feature of PCSK9 and not limited to peptides. Because the helix provides a constrained spatial orientation of the missense mutations and the posttranslationally modified residues, it is probable that their biological functions take place in the context of an ordered conformational state.


    Organizational Affiliation

    Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Biomolecular Resources, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: dak@gene.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anti-PCSK9 fab 6E2 heavy chain
H
224N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Anti-PCSK9 fab 6E2 light chain
L
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proprotein convertase subtilisin/kexin type 9
P
23Homo 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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
H, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
H, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NEP
Query on NEP
H
L-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
ACE
Query on ACE
P
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.449α = 90.00
b = 100.420β = 90.00
c = 86.590γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release