7E6P | pdb_00007e6p

Fab-amyloid beta fragment complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.244 (Depositor), 0.168 (DCC) 
  • R-Value Work: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7E6P

This is version 1.1 of the entry. See complete history

Literature

Characterization of a Conformation-Restricted Amyloid beta Peptide and Immunoreactivity of Its Antibody in Human AD brain.

Kageyama, Y.Irie, Y.Matsushima, Y.Segawa, T.Bellier, J.P.Hidaka, K.Sugiyama, H.Kaneda, D.Hashizume, Y.Akatsu, H.Miki, K.Kita, A.Walker, D.G.Irie, K.Tooyama, I.

(2021) ACS Chem Neurosci 12: 3418-3432

  • DOI: https://doi.org/10.1021/acschemneuro.1c00416
  • Primary Citation Related Structures: 
    7E6P

  • PubMed Abstract: 

    Characterization of amyloid β (Aβ) oligomers, the transition species present prior to the formation of Aβ fibrils and that have cytotoxicity, has become one of the major topics in the investigations of Alzheimer's disease (AD) pathogenesis. However, studying pathophysiological properties of Aβ oligomers is challenging due to the instability of these protein complexes in vitro . Here, we report that conformation-restricted Aβ42 with an intramolecular disulfide bond at positions 17 and 28 (SS-Aβ42) formed stable Aβ oligomers in vitro . Thioflavin T binding assays, nondenaturing gel electrophoresis, and morphological analyses revealed that SS-Aβ42 maintained oligomeric structure, whereas wild-type Aβ42 and the highly aggregative Aβ42 mutant with E22P substitution (E22P-Aβ42) formed Aβ fibrils. In agreement with these observations, SS-Aβ42 was more cytotoxic compared to the wild-type and E22P-Aβ42 in cell cultures. Furthermore, we developed a monoclonal antibody, designated TxCo-1, using the toxic conformation of SS-Aβ42 as immunogen. X-ray crystallography of the TxCo-1/SS-Aβ42 complex, enzyme immunoassay, and immunohistochemical studies confirmed the recognition site and specificity of TxCo-1 to SS-Aβ42. Immunohistochemistry with TxCo-1 antibody identified structures resembling senile plaques and vascular Aβ in brain samples of AD subjects. However, TxCo-1 immunoreactivity did not colocalize extensively with Aβ plaques identified with conventional Aβ antibodies. Together, these findings indicate that Aβ with a turn at positions 22 and 23, which is prone to form Aβ oligomers, could show strong cytotoxicity and accumulated in brains of AD subjects. The SS-Aβ42 and TxCo-1 antibody should facilitate understanding of the pathological role of Aβ with toxic conformation in AD.


  • Organizational Affiliation
    • Molecular Neuroscience Research Center, Shiga University of Medical Science, Shiga 520-2192, Japan.

Macromolecule Content 

  • Total Structure Weight: 50.18 kDa 
  • Atom Count: 3,551 
  • Modeled Residue Count: 449 
  • Deposited Residue Count: 456 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab Heavy chainA [auth L]220Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab Light chainB [auth H]220Mus musculusMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Amyloid beta fragment with an intramolecular disulfide bond at positions 17 and 28C [auth A]16Homo 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.244 (Depositor), 0.168 (DCC) 
  • R-Value Work:  0.191 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.049α = 90
b = 40.464β = 97.219
c = 69.379γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP19H00921

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-05
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Derived calculations, Structure summary