Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.11 kDa 
• Atom Count: 3272 
• Modelled Residue Count: 371 
• Deposited Residue Count: 409 
• Unique protein chains: 1

3ZOV

CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH CHEMICAL LIGAND

• PDB DOI: 10.2210/pdb3ZOV/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-02-25 Released: 2013-05-29 
• Deposition Author(s): Banner, D.W., Kuglstatter, A., Benz, J., Stihle, M., Ruf, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.272 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Literature

Mapping the Conformational Space Accessible to Bace2 Using Surface Mutants and Co-Crystals with Fab-Fragments, Fynomers, and Xaperones

Banner, D.W., Gsell, B., Benz, J., Bertschinger, J., Burger, D., Brack, S., Cuppuleri, S., Debulpaep, M., Gast, A., Grabulovski, D., Hennig, M., Hilpert, H., Huber, W., Kuglstatter, A., Kusznir, E., Laeremans, T., Matile, H., Miscenic, C., Rufer, A., Schlatter, D., Steyeart, J., Stihle, M., Thoma, R., Weber, M., Ruf, A.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1124

• PubMed: 23695257 
• DOI: 10.1107/S0907444913006574
• Primary Citation of Related Structures:  
  3ZKG, 3ZKI, 3ZKM, 3ZKN, 3ZKQ, 3ZKS, 3ZKX, 3ZL7, 3ZOV, 4BEL, 4BFB


• PubMed Abstract: 
  

The aspartic protease BACE2 is responsible for the shedding of the transmembrane protein Tmem27 from the surface of pancreatic β-cells, which leads to inactivation of the β-cell proliferating activity of Tmem27. This role of BACE2 in the control of β-cell maintenance suggests BACE2 as a drug target for diabetes. Inhibition of BACE2 has recently been shown to lead to improved control of glucose homeostasis and to increased insulin levels in insulin-resistant mice. BACE2 has 52% sequence identity to the well studied Alzheimer's disease target enzyme β-secretase (BACE1). High-resolution BACE2 structures would contribute significantly to the investigation of this enzyme as either a drug target or anti-target. Surface mutagenesis, BACE2-binding antibody Fab fragments, single-domain camelid antibody VHH fragments (Xaperones) and Fyn-kinase-derived SH3 domains (Fynomers) were used as crystallization helpers to obtain the first high-resolution structures of BACE2. Eight crystal structures in six different packing environments define an ensemble of low-energy conformations available to the enzyme. Here, the different strategies used for raising and selecting BACE2 binders for cocrystallization are described and the crystallization success, crystal quality and the time and resources needed to obtain suitable crystals are compared.

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Organizational Affiliation: 

pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-SECRETASE 1	A	409	Homo sapiens	Mutation(s): 1  Gene Names: BACE1, BACE, KIAA1149 EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens) Explore P56817  Go to UniProtKB:  P56817
PHAROS:  P56817

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WZV	B [auth A]	5-(2,2,2-Trifluoro-ethoxy)-pyridine-2-carboxylic acid [3-((S)-2-amino-1,4-dimethyl-6-oxo-1,4,5,6-tetrahydro-pyrimidin-4-yl)-phenyl]-amide C20 H20 F3 N5 O3 ZJFIBYCNZHIVEL-IBGZPJMESA-N
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
WZV	PDBBind:  3ZOV	IC50: 60 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.272 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.571	α = 90
b = 102.571	β = 90
c = 171.32	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-25 
• Released Date: 2013-05-29 
Deposition Author(s): Banner, D.W., Kuglstatter, A., Benz, J., Stihle, M., Ruf, A.

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2013-06-05
  Changes: Database references
• Version 1.2: 2019-01-30
  Changes: Data collection, Experimental preparation
• Version 1.3: 2019-02-06
  Changes: Data collection, Experimental preparation