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: 18.78 kDa 
• Atom Count: 884 
• Modelled Residue Count: 101 
• Deposited 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

• PDB DOI: 10.2210/pdb4JFN/pdb

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


• 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 
• R-Value Observed: 0.183 

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
• Primary Citation of Related Structures:  
  4JFN


• 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, [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid beta A4 protein	A	163	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU	B [auth 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 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.05	α = 90
b = 49.07	β = 90
c = 66.16	γ = 90

Software Package:

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

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
  Changes: Database references