Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6941.02 
• Atom Count: 498 
• Residue Count: 59 
• Unique protein chains: 1

2FMA

Structure of the Alzheimer's Amyloid Precursor Protein (APP) Copper Binding Domain in 'small unit cell' form, atomic resolution

• DOI: 10.2210/pdb2FMA/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris


• Deposited: 2006-01-08 Released: 2007-01-16 
• Deposition Author(s): Kong, G.K.-W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.85 Å
• R-Value Free: 0.150 
• R-Value Work: 0.131 

Literature

Structure of Alzheimer's disease amyloid precursor protein copper-binding domain at atomic resolution.

Kong, G.K., Adams, J.J., Cappai, R., Parker, M.W.

(2007) Acta Crystallogr.,Sect.F 63: 819-824

• PubMed: 17909280 
• DOI: 10.1107/S1744309107041139


• PubMed Abstract: 
  

Amyloid precursor protein (APP) plays a central role in the pathogenesis of Alzheimer's disease, as its cleavage generates the Abeta peptide that is toxic to cells. APP is able to bind Cu2+ and reduce it to Cu+ through its copper-binding domain (CuBD). The interaction between Cu2+ and APP leads to a decrease in Abeta production and to alleviation of the symptoms of the disease in mouse models. Structural studies of CuBD have been undertaken in order to better understand the mechanism behind the process. Here, the crystal structure of CuBD in the metal-free form determined to ultrahigh resolution (0.85 A) is reported. The structure shows that the copper-binding residues of CuBD are rather rigid but that Met170, which is thought to be the electron source for Cu2+ reduction, adopts two different side-chain conformations. These observations shed light on the copper-binding and redox mechanisms of CuBD. The structure of CuBD at atomic resolution provides an accurate framework for structure-based design of molecules that will deplete Abeta production.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Amyloid beta A4 protein precursor	A	59	Homo sapiens	Mutation(s): 0  Gene Names: APP (A4, AD1)
Find proteins for P05067 (Homo sapiens) Go to Gene View: APP Go to UniProtKB:  P05067

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.85 Å
• R-Value Free: 0.150 
• R-Value Work: 0.131 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 31.289	α = 90.00
b = 32.488	β = 90.00
c = 50.088	γ = 90.00

Software Package:

Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
SHELX	phasing
SHELX	model building
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-01-08 
• Released Date: 2007-01-16 
• Deposition Author(s): Kong, G.K.-W.

Revision History 

• Version 1.0: 2007-01-16
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance