4YN0

Crystal structure of APP E2 domain in complex with DR6 CRD domain

  • Classification: Apoptosis/Cell Adhesion
  • Organism(s): Mus musculus
  • Expression System: Homo sapiens

  • Deposited: 2015-03-08 Released: 2015-04-15 
  • Deposition Author(s): Xu, K., Nikolov, D.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; Department of Energy (United States) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of DR6 in complex with the amyloid precursor protein provides insight into death receptor activation.

Xu, K.Olsen, O.Tzvetkova-Robev, D.Tessier-Lavigne, M.Nikolov, D.B.

(2015) Genes Dev. 29: 785-790

  • DOI: 10.1101/gad.257675.114

  • PubMed Abstract: 
  • The amyloid precursor protein (APP) has garnered considerable attention due to its genetic links to Alzheimer's disease. Death receptor 6 (DR6) was recently shown to bind APP via the protein extracellular regions, stimulate axonal pruning, and inhibi ...

    The amyloid precursor protein (APP) has garnered considerable attention due to its genetic links to Alzheimer's disease. Death receptor 6 (DR6) was recently shown to bind APP via the protein extracellular regions, stimulate axonal pruning, and inhibit synapse formation. Here, we report the crystal structure of the DR6 ectodomain in complex with the E2 domain of APP and show that it supports a model for APP-induced dimerization and activation of cell surface DR6.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor receptor superfamily member 21
A
190Mus musculusGene Names: Tnfrsf21 (Dr6)
Find proteins for Q9EPU5 (Mus musculus)
Go to UniProtKB:  Q9EPU5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Amyloid beta A4 protein
B
233Mus musculusGene Names: App
Find proteins for P12023 (Mus musculus)
Go to UniProtKB:  P12023
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.226 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 67.320α = 90.00
b = 67.320β = 90.00
c = 226.229γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-03-08 
  • Released Date: 2015-04-15 
  • Deposition Author(s): Xu, K., Nikolov, D.

Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103403
Department of Energy (United States)United StatesDE-AC02-06CH11357

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-04-29
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy