3NYJ

Crystal Structure Analysis of APP E2 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.380 
  • R-Value Work: 0.297 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The E2 Domains of APP and APLP1 Share a Conserved Mode of Dimerization.

Lee, S.Xue, Y.Hu, J.Wang, Y.Liu, X.Demeler, B.Ha, Y.

(2011) Biochemistry 50: 5453-5464

  • DOI: 10.1021/bi101846x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Amyloid precursor protein (APP) is genetically linked to Alzheimer's disease. APP is a type I membrane protein, and its oligomeric structure is potentially important because this property may play a role in its function or affect the processing of th ...

    Amyloid precursor protein (APP) is genetically linked to Alzheimer's disease. APP is a type I membrane protein, and its oligomeric structure is potentially important because this property may play a role in its function or affect the processing of the precursor by the secretases to generate amyloid β-peptide. Several independent studies have shown that APP can form dimers in the cell, but how it dimerizes remains controversial. At least three regions of the precursor, including a centrally located and conserved domain called E2, have been proposed to contribute to dimerization. Here we report two new crystal structures of E2, one from APP and the other from APLP1, a mammalian APP homologue. Comparison with an earlier APP structure, which was determined in a different space group, shows that the E2 domains share a conserved and antiparallel mode of dimerization. Biophysical measurements in solution show that heparin binding induces E2 dimerization. The 2.1 Å resolution electron density map also reveals phosphate ions that are bound to the protein surface. Mutational analysis shows that protein residues interacting with the phosphate ions are also involved in heparin binding. The locations of two of these residues, Arg-369 and His-433, at the dimeric interface suggest a mechanism for heparin-induced protein dimerization.


    Organizational Affiliation

    Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Amyloid beta A4 protein
A
207Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OS
Query on OS

Download SDF File 
Download CCD File 
A
OSMIUM ION
Os
XQBKHDFIPARBOX-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.380 
  • R-Value Work: 0.297 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 114.979α = 90.00
b = 40.149β = 90.00
c = 58.376γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
CBASSdata collection
DMphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description