5MYO

Structure of Pyroglutamate-Abeta-specific Fab c#6 in complex with human Abeta-pE3-12-PEGb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  5MY4, 5MYK, 5MYX

  • 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 in vitro and in vivo Because N-terminally truncate ...

    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 (AβpE3) 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 AβpE3 with affinities of 1-10 nm and inhibit AβpE3 fibril formation in vitro. In vivo application of one of these resulted in improved memory in AβpE3 oligomer-treated mice. Crystal structures of Fab-AβpE3 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 AβpE3 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

    From Probiodrug AG, Weinbergweg 22, 06120 Halle (Saale), Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab c#6 light chain
A, C
219N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab c#6 heavy chain
B, D
228N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Amyloid beta A4 protein
E
10Homo sapiensGene Names: APP (A4, AD1)
Find proteins for P05067 (Homo sapiens)
Go to Gene View: APP
Go to UniProtKB:  P05067
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
E
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 53.774α = 62.87
b = 65.958β = 82.93
c = 67.760γ = 84.11
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction
XSCALEdata scaling

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