5MY4

Structure of Pyroglutamate-Abeta-specific Fab c#17 in complex with human Abeta-pE3-12PEGb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.211 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and functional analyses of pyroglutamate-amyloid-beta-specific antibodies as a basis for Alzheimer immunotherapy.

Piechotta, A.Parthier, C.Kleinschmidt, M.Gnoth, K.Pillot, T.Lues, I.Demuth, H.U.Schilling, S.Rahfeld, J.U.Stubbs, M.T.

(2017) J. Biol. Chem. 292: 12713-12724

  • DOI: 10.1074/jbc.M117.777839
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Alzheimer disease is associated with deposition of the amyloidogenic peptide Aβ in the brain. Passive immunization using Aβ-specific antibodies has been demonstrated to reduce amyloid deposition both <i>in vitro </i> and <i>in vivo </i> Because N-t ...

    Alzheimer disease is associated with deposition of the amyloidogenic peptide Aβ in the brain. Passive immunization using Aβ-specific antibodies has been demonstrated to reduce amyloid deposition both in vitro and in vivo Because N-terminally truncated pyroglutamate (pE)-modified Aβ species (Aβ pE3 ) exhibit enhanced aggregation potential and propensity to form toxic oligomers, they represent particularly attractive targets for antibody therapy. Here we present three separate monoclonal antibodies that specifically recognize Aβ pE3 with affinities of 1-10 nm and inhibit Aβ pE3 fibril formation in vitro. In vivo application of one of these resulted in improved memory in Aβ pE3 oligomer-treated mice. Crystal structures of F ab -Aβ pE3 complexes revealed two distinct binding modes for the peptide. Juxtaposition of pyroglutamate pE3 and the F4 side chain (the "pEF head") confers a pronounced bulky hydrophobic nature to the Aβ pE3 N terminus that might explain the enhanced aggregation properties of the modified peptide. The deep burial of the pEF head by two of the antibodies explains their high target specificity and low cross-reactivity, making them promising candidates for the development of clinical antibodies.


    Organizational Affiliation

    the Institute of Biotechnology, Martin Luther University, 06108 Halle-Wittenberg, Germany, stubbs@biochemtech.uni-halle.de.,From Probiodrug AG, Weinbergweg 22, 06120 Halle (Saale), Germany.,From Probiodrug AG, Weinbergweg 22, 06120 Halle (Saale), Germany, jens-ulrich.rahfeld@probiodrug.de.,the Institute of Biotechnology, Martin Luther University, 06108 Halle-Wittenberg, Germany.,the Department of Molecular Drug Biochemistry and Therapy, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany, and.,SynAging SAS, 54518 Vandoeuvre-les-Nancy, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab c#17 light chain
A
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab c#17 heavy chain
B
231N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pyroglutamate-Abeta pE3-12-PEGb
C
10Homo sapiensMutation(s): 0 
Gene Names: APP (A4, AD1)
Find proteins for P05067 (Homo sapiens)
Go to Gene View: APP
Go to UniProtKB:  P05067
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
C
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.211 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.170α = 90.00
b = 87.142β = 96.06
c = 58.029γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Database references
  • Version 1.2: 2017-10-11
    Type: Data collection