Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 22284.24 
• Atom Count: 1441 
• Residue Count: 196 
• 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): 19 


• 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: 1.5 Å
• R-Value Free: 0.186 
• R-Value Work: 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:  
  4MVL, 4MVI


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Neutrophil gelatinase-associated lipocalin	A	188	Homo sapiens	Mutation(s): 19  Gene Names: LCN2 (HNL, NGAL)
Find proteins for P80188 (Homo sapiens) Go to Gene View: LCN2 Go to UniProtKB:  P80188

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Amyloid peptide fragment VFFAED	B	8	Homo sapiens	Mutation(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  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NH2	B	NON-POLYMER	H2 N		--
ACE	B	NON-POLYMER	C2 H4 O		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.186 
• R-Value Work: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 50.970	α = 90.00
b = 59.230	β = 90.00
c = 61.230	γ = 90.00

Software Package:

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

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
  Type: Database references
• Version 1.2: 2016-06-15
  Type: Database references