Crystal structure of an engineered lipocalin (Anticalin US7) in complex with the Alzheimer amyloid peptide fragment VFFAED

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


High-affinity Anticalins with aggregation-blocking activity directed against the Alzheimer beta-amyloid peptide.

Rauth, S.Hinz, D.Borger, M.Uhrig, M.Mayhaus, M.Riemenschneider, M.Skerra, A.

(2016) Biochem J 473: 1563-1578

  • DOI: https://doi.org/10.1042/BCJ20160114
  • Primary Citation of Related Structures:  
    4MVI, 4MVK, 4MVL

  • PubMed Abstract: 

    Amyloid beta (Aβ) peptides, in particular Aβ42 and Aβ40, exert neurotoxic effects and their overproduction leads to amyloid deposits in the brain, thus constituting an important biomolecular target for treatments of Alzheimer's disease (AD). We describe the engineering of cognate Anticalins as a novel type of neutralizing protein reagent based on the human lipocalin scaffold. Phage display selection from a genetic random library comprising variants of the human lipocalin 2 (Lcn2) with mutations targeted at 20 exposed amino acid positions in the four loops that form the natural binding site was performed using both recombinant and synthetic target peptides and resulted in three different Anticalins. Biochemical characterization of the purified proteins produced by periplasmic secretion in Escherichia coli revealed high folding stability in a monomeric state, with Tm values ranging from 53.4°C to 74.5°C, as well as high affinities for Aβ40, between 95 pM and 563 pM, as measured by real-time surface plasmon resonance analysis. The central linear VFFAED epitope within the Aβ sequence was mapped using a synthetic peptide array on membranes and was shared by all three Anticalins, despite up to 13 mutual amino acid differences in their binding sites. All Anticalins had the ability-with varying extent-to inhibit Aβ aggregation in vitro according to the thioflavin-T fluorescence assay and, furthermore, they abolished Aβ42-mediated toxicity in neuronal cell culture. Thus, these Anticalins provide not only useful protein reagents to study the molecular pathology of AD but they also show potential as alternative drug candidates compared with antibodies.

  • Organizational Affiliation

    Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising (Weihenstephan), Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutrophil gelatinase-associated lipocalin188Homo sapiensMutation(s): 19 
Gene Names: engineered variant US7HNLLCN2LCN2 (NGAL_HUMAN)NGAL
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens)
Explore P80188 
Go to UniProtKB:  P80188
PHAROS:  P80188
GTEx:  ENSG00000148346 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80188
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Amyloid peptide fragment VFFAED8Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens)
Explore P05067 
Go to UniProtKB:  P05067
PHAROS:  P05067
GTEx:  ENSG00000142192 
Entity Groups  
UniProt GroupP05067
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.97α = 90
b = 59.23β = 90
c = 61.23γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2016-06-15
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description