Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.28 kDa 
• Atom Count: 1598 
• Residue Count: 179 
• Unique protein chains: 2

4MVK

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

• DOI: 10.2210/pdb4MVK/pdb

• Classification: PROTEIN BINDING/PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-09-24 Released: 2015-08-12 
• Deposition Author(s): Eichinger, A., Skerra, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.186 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 

Literature

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

• PubMed: 27029347 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil gelatinase-associated lipocalin	A	188	Homo sapiens	Mutation(s): 19  Gene Names: engineered variant US7, HNL, LCN2, LCN2 (NGAL_HUMAN), NGAL
Find proteins for P80188 (Homo sapiens) Explore P80188  Go to UniProtKB:  P80188
NIH Common Fund Data Resources
PHAROS  P80188 GTEx  ENSG00000148346

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid peptide fragment VFFAED	B	8	Homo sapiens	Mutation(s): 0  Gene Names: APP, A4, AD1
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
NIH Common Fund Data Resources
PHAROS  P05067

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 50.97	α = 90
b = 59.23	β = 90
c = 61.23	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-24 
• Released Date: 2015-08-12 
Deposition Author(s): Eichinger, A., Skerra, A.

Revision History 

• 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