4RDA

X-RAY STRUCTURE OF THE AMYLOID PRECURSOR PROTEIN-LIKE PROTEIN 1 (APLP1) E2 DOMAIN IN COMPLEX WITH A HEPARIN DODECASACCHARIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.497 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Interaction of the amyloid precursor protein-like protein 1 (APLP1) E2 domain with heparan sulfate involves two distinct binding modes.

Dahms, S.O.Mayer, M.C.Roeser, D.Multhaup, G.Than, M.E.

(2015) Acta Crystallogr.,Sect.D 71: 494-504

  • DOI: 10.1107/S1399004714027114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Beyond the pathology of Alzheimer's disease, the members of the amyloid precursor protein (APP) family are essential for neuronal development and cell homeostasis in mammals. APP and its paralogues APP-like protein 1 (APLP1) and APP-like protein 2 (A ...

    Beyond the pathology of Alzheimer's disease, the members of the amyloid precursor protein (APP) family are essential for neuronal development and cell homeostasis in mammals. APP and its paralogues APP-like protein 1 (APLP1) and APP-like protein 2 (APLP2) contain the highly conserved heparan sulfate (HS) binding domain E2, which effects various (patho)physiological functions. Here, two crystal structures of the E2 domain of APLP1 are presented in the apo form and in complex with a heparin dodecasaccharide at 2.5 Å resolution. The apo structure of APLP1 E2 revealed an unfolded and hence flexible N-terminal helix αA. The (APLP1 E2)2-(heparin)2 complex structure revealed two distinct binding modes, with APLP1 E2 explicitly recognizing the heparin terminus but also interacting with a continuous heparin chain. The latter only requires a certain register of the sugar moieties that fits to a positively charged surface patch and contributes to the general heparin-binding capability of APP-family proteins. Terminal binding of APLP1 E2 to heparin specifically involves a structure of the nonreducing end that is very similar to heparanase-processed HS chains. These data reveal a conserved mechanism for the binding of APP-family proteins to HS and imply a specific regulatory role of HS modifications in the biology of APP and APP-like proteins.


    Organizational Affiliation

    Protein Crystallography Group, Leibniz Institute for Age Research (FLI), Beutenbergstrasse 11, 07745 Jena, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Amyloid-like protein 1
A, B
210Homo sapiensMutation(s): 0 
Gene Names: APLP1
Find proteins for P51693 (Homo sapiens)
Go to Gene View: APLP1
Go to UniProtKB:  P51693
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SGN
Query on SGN

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Download CCD File 
A, B
N,O6-DISULFO-GLUCOSAMINE
C6 H13 N O11 S2
DQTRACMFIGDHSN-UKFBFLRUSA-N
 Ligand Interaction
UAP
Query on UAP

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Download CCD File 
A
4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid
C6 H8 O9 S
VJIMUKBSNUBECH-YKKSOZKNSA-N
 Ligand Interaction
IDS
Query on IDS

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Download CCD File 
A, B
2-O-sulfo-alpha-L-idopyranuronic acid
O2-SULFO-GLUCURONIC ACID
C6 H10 O10 S
COJBCAMFZDFGFK-VCSGLWQLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.497 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.216 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.969α = 90.00
b = 91.969β = 90.00
c = 208.481γ = 120.00
Software Package:
Software NamePurpose
SHARPphasing
MxCuBEdata collection
XDSdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-03-18
    Type: Database references