3NYL

The X-ray structure of an antiparallel dimer of the human amyloid precursor protein E2 domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

The X-ray structure of an antiparallel dimer of the human amyloid precursor protein E2 domain.

Wang, Y., Ha, Y.

(2004) Mol Cell 15: 343-353

  • DOI: 10.1016/j.molcel.2004.06.037
  • Primary Citation of Related Structures:  
    3NYL

  • PubMed Abstract: 

    • Amyloid beta-peptide, which forms neuronal and vascular amyloid deposits in Alzheimer's disease, is derived from an integral membrane protein precursor. The biological function of the precursor is currently unclear. Here we describe the X-ray structure of E2, the largest of the three conserved domains of the precursor ...

    Amyloid beta-peptide, which forms neuronal and vascular amyloid deposits in Alzheimer's disease, is derived from an integral membrane protein precursor. The biological function of the precursor is currently unclear. Here we describe the X-ray structure of E2, the largest of the three conserved domains of the precursor. The structure of E2 consists of two coiled-coil substructures connected through a continuous helix and bears an unexpected resemblance to the spectrin family of protein structures. E2 can reversibly dimerize in the solution, and the dimerization occurs along the longest dimension of the molecule in an antiparallel orientation, which enables the N-terminal substructure of one monomer to pack against the C-terminal substructure of a second monomer. Heparan sulfate proteoglycans, the putative ligand for the precursor present in extracellular matrix, bind to E2 at a conserved and positively charged site near the dimer interface.

    Organizational Affiliation: 

    Department of Pharmacology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Amyloid beta (A4) protein (Peptidase nexin-II, Alzheimer disease), isoform CRA_bA210Homo sapiensMutation(s): 0 
Gene Names: APP, hCG_1810805, A4, AD1
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens)
Explore P05067 
Go to UniProtKB:  P05067
PHAROS:  P05067
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05067
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.265 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.589α = 90
b = 83.589β = 90
c = 147.341γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLVEphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-13
    Type: Initial release