Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.85 kDa 
• Atom Count: 594 
• Modelled Residue Count: 59 
• Deposited Residue Count: 59 
• Unique protein chains: 1

2FJZ

Structure of the Alzheimer's Amyloid Precursor Protein (APP) copper binding domain (residues 133 to 189) in 'small unit cell' form, metal-free

• PDB DOI: 10.2210/pdb2FJZ/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2006-01-03 Released: 2007-01-16 
• Deposition Author(s): Kong, G.K.-W., Parker, M.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.209 
• R-Value Work: 0.177 
• R-Value Observed: 0.177 

Literature

Structural Studies of the Alzheimer's Amyloid Precursor Protein Copper-binding Domain Reveal How it Binds Copper Ions

Kong, G.K., Adams, J.J., Harris, H.H., Boas, J.F., Curtain, C.C., Galatis, D., Masters, C.L., Barnham, K.J., McKinstry, W.J., Cappai, R., Parker, M.W.

(2007) J Mol Biol 367: 148-161

• PubMed: 17239395 
• DOI: 10.1016/j.jmb.2006.12.041
• Primary Citation of Related Structures:  
  2FJZ, 2FK1, 2FK2, 2FK3, 2FKL


• PubMed Abstract: 
  

Alzheimer's disease (AD) is the major cause of dementia. Amyloid beta peptide (Abeta), generated by proteolytic cleavage of the amyloid precursor protein (APP), is central to AD pathogenesis. APP can function as a metalloprotein and modulate copper (Cu) transport, presumably via its extracellular Cu-binding domain (CuBD). Cu binding to the CuBD reduces Abeta levels, suggesting that a Cu mimetic may have therapeutic potential. We describe here the atomic structures of apo CuBD from three crystal forms and found they have identical Cu-binding sites despite the different crystal lattices. The structure of Cu(2+)-bound CuBD reveals that the metal ligands are His147, His151, Tyr168 and two water molecules, which are arranged in a square pyramidal geometry. The site resembles a Type 2 non-blue Cu center and is supported by electron paramagnetic resonance and extended X-ray absorption fine structure studies. A previous study suggested that Met170 might be a ligand but we suggest that this residue plays a critical role as an electron donor in CuBDs ability to reduce Cu ions. The structure of Cu(+)-bound CuBD is almost identical to the Cu(2+)-bound structure except for the loss of one of the water ligands. The geometry of the site is unfavorable for Cu(+), thus providing a mechanism by which CuBD could readily transfer Cu ions to other proteins.

---

Organizational Affiliation: 

Biota Structural Biology Laboratory, St. Vincent's Institute, 9 Princes Street, Fitzroy, Victoria 3065, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid beta A4 protein precursor	A	59	Homo sapiens	Mutation(s): 0  Gene Names: APP, A4, AD1
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
PHAROS:  P05067

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.209 
• R-Value Work: 0.177 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.346	α = 90
b = 32.518	β = 90
c = 50.2	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-01-03 
• Released Date: 2007-01-16 
Deposition Author(s): Kong, G.K.-W., Parker, M.W.

Revision History  

• Version 1.0: 2007-01-16
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection