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RCSB PDB
233,605 Structures from the PDB
1,068,577 Computed Structure Models (CSM)
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 2OTK|pdb_00002otk

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


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 

wwPDB Validation  3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • PubMed18375754 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1073/pnas.0711731105
  • Primary Citation of Related Structures:  
    2OTK

  • 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.


  • Organizational Affiliation

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

Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Validation Report


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 
Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Find Similar Assemblies

Biological assembly 1 assigned by authors.

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Macromolecule Content

  • Total Structure Weight: 19.97 kDa 
  • Atom Count: 833 
  • Modelled Residue Count: 111 
  • Deposited Residue Count: 182 
  • Unique protein chains: 2

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amyloid beta A4 proteinA [auth C]40Homo 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 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05067
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ZAb3 Affibody dimerB [auth E],
C [auth F]
71N/AMutation(s): 0 
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
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 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.


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