8FQ7

Nanobody with WIW inserted in CDR3 loop to Inhibit Growth of Alzheimer's Tau fibrils


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-based design of nanobodies that inhibit seeding of Alzheimer's patient-extracted tau fibrils.

Abskharon, R.Pan, H.Sawaya, M.R.Seidler, P.M.Olivares, E.J.Chen, Y.Murray, K.A.Zhang, J.Lantz, C.Bentzel, M.Boyer, D.R.Cascio, D.Nguyen, B.A.Hou, K.Cheng, X.Pardon, E.Williams, C.K.Nana, A.L.Vinters, H.V.Spina, S.Grinberg, L.T.Seeley, W.W.Steyaert, J.Glabe, C.G.Ogorzalek Loo, R.R.Loo, J.A.Eisenberg, D.S.

(2023) Proc Natl Acad Sci U S A 120: e2300258120-e2300258120

  • DOI: https://doi.org/10.1073/pnas.2300258120
  • Primary Citation of Related Structures:  
    8FQ7

  • PubMed Abstract: 

    Despite much effort, antibody therapies for Alzheimer's disease (AD) have shown limited efficacy. Challenges to the rational design of effective antibodies include the difficulty of achieving specific affinity to critical targets, poor expression, and antibody aggregation caused by buried charges and unstructured loops. To overcome these challenges, we grafted previously determined sequences of fibril-capping amyloid inhibitors onto a camel heavy chain antibody scaffold. These sequences were designed to cap fibrils of tau, known to form the neurofibrillary tangles of AD, thereby preventing fibril elongation. The nanobodies grafted with capping inhibitors blocked tau aggregation in biosensor cells seeded with postmortem brain extracts from AD and progressive supranuclear palsy (PSP) patients. The tau capping nanobody inhibitors also blocked seeding by recombinant tau oligomers. Another challenge to the design of effective antibodies is their poor blood-brain barrier (BBB) penetration. In this study, we also designed a bispecific nanobody composed of a nanobody that targets a receptor on the BBB and a tau capping nanobody inhibitor, conjoined by a flexible linker. We provide evidence that the bispecific nanobody improved BBB penetration over the tau capping inhibitor alone after intravenous administration in mice. Our results suggest that the design of synthetic antibodies that target sequences that drive protein aggregation may be a promising approach to inhibit the prion-like seeding of tau and other proteins involved in AD and related proteinopathies.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody with WIW insert in CDR3 loop to target tau fibrils126Camelus dromedariusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.29α = 90
b = 78.29β = 90
c = 38.22γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United States1R01AG070895
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United States1F32 NS095661

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Database references