Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - ABCD Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer -A2BC 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 119575.63 
• Atom Count: 7628 
• Residue Count: 1121 
• Unique protein chains: 4

3H42

Crystal structure of PCSK9 in complex with Fab from LDLR competitive antibody

• DOI: 10.2210/pdb3H42/pdb

• Classification: HYDROLASE/IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Trichoplusia ni
• Mutation(s): 1 


• Deposited: 2009-04-17 Released: 2009-05-05 
• Deposition Author(s): Piper, D.E., Walker, N.P.C., Romanow, W.G., Thibault, S.T., Tsai, M.M., Yang, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.209 
• R-Value Work: 0.191 

Literature

From the Cover: A proprotein convertase subtilisin/kexin type 9 neutralizing antibody reduces serum cholesterol in mice and nonhuman primates.

Chan, J.C., Piper, D.E., Cao, Q., Liu, D., King, C., Wang, W., Tang, J., Liu, Q., Higbee, J., Xia, Z., Di, Y., Shetterly, S., Arimura, Z., Salomonis, H., Romanow, W.G., Thibault, S.T., Zhang, R., Cao, P., Yang, X.P., Yu, T., Lu, M., Retter, M.W., Kwon, G., Henne, K., Pan, O., Tsai, M.M., Fuchslocher, B., Yang, E., Zhou, L., Lee, K.J., Daris, M., Sheng, J., Wang, Y., Shen, W.D., Yeh, W.C., Emery, M., Walker, N.P., Shan, B., Schwarz, M., Jackson, S.M.

(2009) Proc.Natl.Acad.Sci.USA 106: 9820-9825

• PubMed: 19443683 
• DOI: 10.1073/pnas.0903849106


• PubMed Abstract: 
  

Proprotein convertase subtilisin/kexin type 9 (PCSK9) regulates serum LDL cholesterol (LDL-C) by interacting with the LDL receptor (LDLR) and is an attractive therapeutic target for LDL-C lowering. We have generated a neutralizing anti-PCSK9 antibody, mAb1, that binds to an epitope on PCSK9 adjacent to the region required for LDLR interaction. In vitro, mAb1 inhibits PCSK9 binding to the LDLR and attenuates PCSK9-mediated reduction in LDLR protein levels, thereby increasing LDL uptake. A combination of mAb1 with a statin increases LDLR levels in HepG2 cells more than either treatment alone. In wild-type mice, mAb1 increases hepatic LDLR protein levels approximately 2-fold and lowers total serum cholesterol by up to 36%: this effect is not observed in LDLR(-/-) mice. In cynomolgus monkeys, a single injection of mAb1 reduces serum LDL-C by 80%, and a significant decrease is maintained for 10 days. We conclude that anti-PCSK9 antibodies may be effective therapeutics for treating hypercholesterolemia.

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Organizational Affiliation: 

Department of Metabolic Disorders, Amgen Inc., South San Francisco, CA 94080, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Proprotein convertase subtilisin/kexin type 9	A	126	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Proprotein convertase subtilisin/kexin type 9	B	540	Homo sapiens	Mutation(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: 3
Molecule	Chains	Sequence Length	Organism	Details
Fab from LDLR competitive antibody: Light chain	L	217	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Fab from LDLR competitive antibody: Heavy chain	H	238	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.209 
• R-Value Work: 0.191 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 264.721	α = 90.00
b = 137.352	β = 102.84
c = 69.885	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SCALA	data scaling
ADSC	data collection
MOSFLM	data reduction
CNS	refinement
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-04-17 
• Released Date: 2009-05-05 
• Deposition Author(s): Piper, D.E., Walker, N.P.C., Romanow, W.G., Thibault, S.T., Tsai, M.M., Yang, E.

Revision History 

• Version 1.0: 2009-05-05
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance