9B4I | pdb_00009b4i

Filament of D-TLKIVWI, a D-peptide that disaggregates Alzheimer's Paired Helical Filaments, determined by Cryo-EM

• PDB DOI: https://doi.org/10.2210/pdb9B4I/pdb
• EM Map EMD-44181: EMDB EMDataResource

• Classification: UNKNOWN FUNCTION
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2024-03-20 Released: 2025-03-12 
• Deposition Author(s): Hou, K., Ge, P., Sawaya, M.R., Eisenberg, D.S.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

How short peptides disassemble tau fibrils in Alzheimer's disease.

Hou, K., Ge, P., Sawaya, M.R., Lutter, L., Dolinsky, J.L., Yang, Y., Jiang, Y.X., Boyer, D.R., Cheng, X., Pi, J., Zhang, J., Lu, J., Abskharon, R., Yang, S., Yu, Z., Feigon, J., Eisenberg, D.S.

(2025) Nature 644: 1020-1027

• PubMed: 40634605 
• DOI: https://doi.org/10.1038/s41586-025-09244-z
• Primary Citation of Related Structures:  
  9B4I, 9B4J, 9B4K, 9B4L, 9B4M, 9B4N, 9B4O


• PubMed Abstract: 
  

  Reducing fibrous aggregates of the protein tau is a possible strategy for halting the progression of Alzheimer's disease (AD) ¹ . Previously, we found that in vitro, the D-enantiomeric peptide (D-peptide) D-TLKIVWC disassembles ultra-stable tau fibrils extracted from the autopsied brains of individuals with AD (hereafter, these tau fibrils are referred to as AD-tau) into benign segments, with no energy source other than ambient thermal agitation ² . To consider D-peptide-mediated disassembly as a potential route to therapeutics for AD, it is essential to understand the mechanism and energy source of the disassembly action. Here, we show that the assembly of D-peptides into amyloid-like ('mock-amyloid') fibrils is essential for AD-tau disassembly. These mock-amyloid fibrils have a right-handed twist but are constrained to adopt a left-handed twist when templated in complex with AD-tau. The release of strain that accompanies the conversion of left-twisted to right-twisted, relaxed mock-amyloid produces a torque that is sufficient to break the local hydrogen bonding between tau molecules, and leads to the fragmentation of AD-tau. This strain-relief mechanism seems to operate in other examples of amyloid fibril disassembly, and could inform the development of first-in-class therapeutics for amyloid diseases.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA. [e-mail].
Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA. [e-mail].
UCLA-DOE Institute, Los Angeles, CA, USA. [e-mail].
Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA. [e-mail].
Howard Hughes Medical Institute, Los Angeles, CA, USA. [e-mail].
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.
UCLA-DOE Institute, Los Angeles, CA, USA.
Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
Howard Hughes Medical Institute, Los Angeles, CA, USA.
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA. [e-mail].
Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA. [e-mail].
UCLA-DOE Institute, Los Angeles, CA, USA. [e-mail].
Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA. [e-mail].
Howard Hughes Medical Institute, Los Angeles, CA, USA. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 52.33 kDa 
• Atom Count: 3,720 
• Modeled Residue Count: 420 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DTH-DLE-DLY-DIL-DVA-DTR-DIL	A, AA [auth 0], AB [auth q], B, BA [auth 1], BB [auth r], C, CA [auth 2], CB [auth s], D, DA [auth 3], DB [auth t], E, EA [auth 4], EB [auth u], F, FA [auth 5], FB [auth v], G, GA [auth 6], GB [auth w], H, HA [auth 7], HB [auth x], I, IA [auth 8], J, JA [auth 9], K, KA [auth a], L, LA [auth b], M, MA [auth c], N, NA [auth d], O, OA [auth e], P, PA [auth f], Q, QA [auth g], R, RA [auth h], S, SA [auth i], T, TA [auth j], U, UA [auth k], V, VA [auth l], W, WA [auth m], X, XA [auth n], Y, YA [auth o], Z, ZA [auth p]	7	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	4

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Hou, K., Ge, P., Sawaya, M.R., Eisenberg, D.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	1R01AG070895
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	RF1AG065407
Department of Energy (DOE, United States)	United States	DOE-FC02-02ERG

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release
  
• Version 1.1: 2025-07-09
  Changes: Data collection, Database references
• Version 1.2: 2025-07-23
  Changes: Data collection, Database references
• Version 1.3: 2025-09-03
  Changes: Data collection, Database references