3K66

X-ray crystal structure of the E2 domain of C. elegans APL-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural characterization of the E2 domain of APL-1, a Caenorhabditis elegans homolog of human amyloid precursor protein, and its heparin binding site

Hoopes, J.T.Liu, X.Xu, X.Demeler, B.Folta-Stogniew, E.Li, C.Ha, Y.

(2010) J Biol Chem 285: 2165-2173

  • DOI: 10.1074/jbc.M109.018432
  • Primary Citation of Related Structures:  
    3K66, 3K6B

  • PubMed Abstract: 
  • The amyloid beta-peptide deposit found in the brain tissue of patients with Alzheimer disease is derived from a large heparin-binding protein precursor APP. The biological function of APP and its homologs is not precisely known. Here we report the x-ray structure of the E2 domain of APL-1, an APP homolog in Caenorhabditis elegans, and compare it to the human APP structure ...

    The amyloid beta-peptide deposit found in the brain tissue of patients with Alzheimer disease is derived from a large heparin-binding protein precursor APP. The biological function of APP and its homologs is not precisely known. Here we report the x-ray structure of the E2 domain of APL-1, an APP homolog in Caenorhabditis elegans, and compare it to the human APP structure. We also describe the structure of APL-1 E2 in complex with sucrose octasulfate, a highly negatively charged disaccharide, which reveals an unexpected binding pocket between the two halves of E2. Based on the crystal structure, we are able to map, using site-directed mutagenesis, a surface groove on E2 to which heparin may bind. Our biochemical data also indicate that the affinity of E2 for heparin is influenced by pH: at pH 5, the binding appears to be much stronger than that at neutral pH. This property is likely caused by histidine residues in the vicinity of the mapped heparin binding site and could be important for the proposed adhesive function of APL-1.


    Related Citations: 
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-amyloid-like proteinA239Caenorhabditis elegansMutation(s): 0 
Gene Names: apl-1C42D8.8
Find proteins for Q10651 (Caenorhabditis elegans)
Explore Q10651 
Go to UniProtKB:  Q10651
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.621α = 90
b = 97.621β = 90
c = 67.975γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL2Mapmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
HKL2Mapphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-10-08 
  • Released Date: 2009-11-10 
  • Deposition Author(s): Hoopes, J.T., Ha, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description