3UMK

X-ray structure of the E2 domain of the human amyloid precursor protein (APP) in complex with copper


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Metal Binding Dictates Conformation and Function of the Amyloid Precursor Protein (APP) E2 Domain.

Dahms, S.O.Konnig, I.Roeser, D.Guhrs, K.H.Mayer, M.C.Kaden, D.Multhaup, G.Than, M.E.

(2012) J.Mol.Biol. 416: 438-452

  • DOI: 10.1016/j.jmb.2011.12.057
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The amyloid precursor protein (APP) and its neurotoxic cleavage product Aβ are key players in the development of Alzheimer's disease and appear essential for neuronal development and cell homeostasis in mammals. Proteolytic processing of APP is influ ...

    The amyloid precursor protein (APP) and its neurotoxic cleavage product Aβ are key players in the development of Alzheimer's disease and appear essential for neuronal development and cell homeostasis in mammals. Proteolytic processing of APP is influenced by metal ions, protein ligands and its oligomerization state. However, the structural basis and functional mechanism of APP regulation are hitherto largely unknown. Here we identified a metal-dependent molecular switch located within the E2 domain of APP containing four evolutionary highly conserved histidine residues. Three X-ray structures of the metal-bound molecule were solved at 2.6-2.0 Å resolution. Using protein crystallographic and biochemical methods, we characterized this novel high-affinity binding site within the E2 domain that binds competitively to copper and zinc at physiological concentrations. Metal-specific coordination spheres induce large conformational changes and enforce distinct structural states, most likely regulating the physiological function of APP and its processing in Alzheimer's disease.


    Organizational Affiliation

    Protein Crystallography Group, Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745 Jena, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Amyloid beta A4 protein
A
211Homo sapiensMutation(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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.206 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 39.760α = 90.00
b = 39.760β = 90.00
c = 126.420γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SHARPphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-02-22
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Advisory, Refinement description