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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18776.02 
• Atom Count: 832 
• Residue Count: 163 
• Unique protein chains: 1

4JFN

Crystal structure of the N-terminal, growth factor-like domain of the amyloid precursor protein bound to copper

• DOI: 10.2210/pdb4JFN/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2013-02-28 Released: 2014-07-23 
• Deposition Author(s): Wild, K., Baumkotter, F., Kins, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.230 
• R-Value Work: 0.181 

Literature

Amyloid precursor protein dimerization and synaptogenic function depend on copper binding to the growth factor-like domain

Baumkotter, F., Schmidt, N., Vargas, C., Schilling, S., Weber, R., Wagner, K., Fiedler, S., Klug, W., Radzimanowski, J., Nickolaus, S., Keller, S., Eggert, S., Wild, K., Kins, S.

(2014) J.Neurosci. 34: 11159-11172

• PubMed: 25122912 
• DOI: 10.1523/JNEUROSCI.0180-14.2014


• PubMed Abstract: 
  

Accumulating evidence suggests that the copper-binding amyloid precursor protein (APP) has an essential synaptic function. APP synaptogenic function depends on trans-directed dimerization of the extracellular E1 domain encompassing a growth factor-like domain (GFLD) and a copper-binding domain (CuBD). Here we report the 1.75 Å crystal structure of the GFLD in complex with a copper ion bound with high affinity to an extended hairpin loop at the dimerization interface. In coimmunoprecipitation assays copper binding promotes APP interaction, whereas mutations in the copper-binding sites of either the GFLD or CuBD result in a drastic reduction in APP cis-orientated dimerization. We show that copper is essential and sufficient to induce trans-directed dimerization of purified APP. Furthermore, a mixed culture assay of primary neurons with HEK293 cells expressing different APP mutants revealed that APP potently promotes synaptogenesis depending on copper binding to the GFLD. Together, these findings demonstrate that copper binding to the GFLD of APP is required for APP cis-/trans-directed dimerization and APP synaptogenic function. Thus, neuronal activity or disease-associated changes in copper homeostasis likely go along with altered APP synaptic function.

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Organizational Affiliation: 

Division of Human Biology and Human Genetics.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Amyloid beta A4 protein	A	163	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 2 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
CU	A	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.230 
• R-Value Work: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 34.050	α = 90.00
b = 49.070	β = 90.00
c = 66.160	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
SCALA	data scaling
MxCuBE	data collection
PHENIX	refinement
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-28 
• Released Date: 2014-07-23 
• Deposition Author(s): Wild, K., Baumkotter, F., Kins, S.

Revision History 

• Version 1.0: 2014-07-23
  Type: Initial release
• Version 1.1: 2014-09-03
  Type: Database references