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
  • Mutation(s): No 

  • 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 (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.4 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
  • Primary Citation of Related Structures:  
    4YN0

  • 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 inhibit synapse formation ...

    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; nikolovd@mskcc.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 21A190Mus musculusMutation(s): 0 
Gene Names: Tnfrsf21Dr6
UniProt
Find proteins for Q9EPU5 (Mus musculus)
Explore Q9EPU5 
Go to UniProtKB:  Q9EPU5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Amyloid beta A4 proteinB233Mus musculusMutation(s): 0 
Gene Names: App
UniProt & NIH Common Fund Data Resources
Find proteins for P12023 (Mus musculus)
Explore P12023 
Go to UniProtKB:  P12023
IMPC:  MGI:88059
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.32α = 90
b = 67.32β = 90
c = 226.229γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

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

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103403
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary