Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.97 kDa 
• Atom Count: 833 
• Residue Count: 111 
• Unique protein chains: 2

2OTK

Structure of Alzheimer Ab peptide in complex with an engineered binding protein

• DOI: 10.2210/pdb2OTK/pdb

• Classification: DE NOVO PROTEIN, PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-08 Released: 2008-02-12 
• Deposition Author(s): Hoyer, W., Hard, T.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 24 
• Selection Criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy 

Literature

Stabilization of a beta-hairpin in monomeric Alzheimer's amyloid-beta peptide inhibits amyloid formation.

Hoyer, W., Gronwall, C., Jonsson, A., Stahl, S., Hard, T.

(2008) Proc Natl Acad Sci U S A 105: 5099-5104

• PubMed: 18375754 
• DOI: 10.1073/pnas.0711731105
• Structures With Same Primary Citation


• PubMed Abstract: 
  

According to the amyloid hypothesis, the pathogenesis of Alzheimer's disease is triggered by the oligomerization and aggregation of the amyloid-beta (Abeta) peptide into protein plaques. Formation of the potentially toxic oligomeric and fibrillar Abeta assemblies is accompanied by a conformational change toward a high content of beta-structure. Here, we report the solution structure of Abeta(1-40) in complex with the phage-display selected affibody protein Z(Abeta3), a binding protein of nanomolar affinity. Bound Abeta(1-40) features a beta-hairpin comprising residues 17-36, providing the first high-resolution structure of Abeta in beta conformation. The positions of the secondary structure elements strongly resemble those observed for fibrillar Abeta. Z(Abeta3) stabilizes the beta-sheet by extending it intermolecularly and by burying both of the mostly nonpolar faces of the Abeta hairpin within a large hydrophobic tunnel-like cavity. Consequently, Z(Abeta3) acts as a stoichiometric inhibitor of Abeta fibrillation. The selected Abeta conformation allows us to suggest a structural mechanism for amyloid formation based on soluble oligomeric hairpin intermediates.

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Related Citations: 

• Selection and characterization of Affibody ligands binding to Alzheimer amyloid beta peptides
  Gronwall, C., Jonsson, A., Lindstrom, S., Gunneriusson, E., Stahl, S., Herne, N.
  (2007) J Biotechnol 128: 162

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Organizational Affiliation: 

Department of Medical Biochemistry and Swedish Nuclear Magnetic Resonance Center, University of Gothenburg, Box 440, SE-405 30 Göteborg, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Amyloid beta A4 protein	C	40	Homo sapiens	Mutation(s): 0  Gene Names: APP, A4, AD1
Find proteins for P05067 (Homo sapiens) Go to UniProtKB:  P05067
NIH Common Fund Data Resources
PHAROS  P05067

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
ZAb3 Affibody dimer	E, F	71	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 24 
• Selection Criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy 
• OLDERADO: 2OTK Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-02-08 
• Released Date: 2008-02-12 
Deposition Author(s): Hoyer, W., Hard, T.

Revision History 

• Version 1.0: 2008-02-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-12-04
  Changes: Data collection, Derived calculations, Experimental preparation, Refinement description