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: 26.09 kDa 
• Atom Count: 1627 
• Modelled Residue Count: 183 
• Deposited Residue Count: 211 
• Unique protein chains: 1

3UMI

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

• PDB DOI: 10.2210/pdb3UMI/pdb

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


• Deposited: 2011-11-13 Released: 2012-01-25 
• Deposition Author(s): Dahms, S.O., Konnig, I., Roeser, D., Guhrs, K.H., Than, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.245 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 

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

• PubMed: 22245578 
• DOI: 10.1016/j.jmb.2011.12.057
• Primary Citation of Related Structures:  
  3UMH, 3UMI, 3UMK


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid beta A4 protein	A	211	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.245 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.757	α = 90
b = 39.757	β = 90
c = 126.425	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-13 
• Released Date: 2012-01-25 
Deposition Author(s): Dahms, S.O., Konnig, I., Roeser, D., Guhrs, K.H., Than, M.E.

Revision History  

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