8XWG | pdb_00008xwg

OspA variants for thioflavin-T binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.281 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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Literature

Redesign of a thioflavin-T-binding protein with a flat beta-sheet to evaluate a thioflavin-T-derived photocatalyst with enhanced affinity.

Miura, Y.Namioka, S.Iwai, A.Yoshida, N.Konno, H.Sohma, Y.Kanai, M.Makabe, K.

(2024) Int J Biol Macromol 269: 131992-131992

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.131992
  • Primary Citation of Related Structures:  
    8XWG

  • PubMed Abstract: 

    Amyloids, proteinous aggregates with β-sheet-rich fibrils, are involved in several neurodegenerative diseases such as Alzheimer's disease; thus, their detection is critically important. The most common fluorescent dye for amyloid detection is thioflavin-T (ThT), which shows on/off fluorescence upon amyloid binding. We previously reported that an engineered globular protein with a flat β-sheet, peptide self-assembly mimic (PSAM), can be used as an amyloid binding model. In this study, we further explored the residue-specific properties of ThT-binding to the flat β-sheet by introducing systematic mutations. We found that site-specific mutations at the ThT-binding channel enhanced affinity. We also evaluated the binding of a ThT-based photocatalyst, which showed the photooxygenation activity on the amyloid fibril upon light radiation. Upon binding of the photocatalyst to the PSAM variant, singlet oxygen-generating activity was observed. The results of this study expand our understanding of the detailed binding mechanism of amyloid-specific molecules.


  • Organizational Affiliation
    • Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer Surface Protein A320Borreliella burgdorferiMutation(s): 4 
UniProt
Find proteins for D0VWU8 (Borreliella burgdorferi)
Explore D0VWU8 
Go to UniProtKB:  D0VWU8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWU8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.281 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.183α = 90
b = 35.807β = 105.99
c = 92.397γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
XDSdata 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)Japan--
Japan Science and TechnologyJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release