8FUG

Alzheimer's disease paired-helical filament in complex with PET tracer GTP-1

  • Classification: PROTEIN FIBRIL
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2023-01-17 Released: 2023-06-07 
  • Deposition Author(s): Merz, G.E., Tse, E., Southworth, D.R.
  • Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Stacked binding of a PET ligand to Alzheimer's tau paired helical filaments.

Merz, G.E.Chalkley, M.J.Tan, S.K.Tse, E.Lee, J.Prusiner, S.B.Paras, N.A.DeGrado, W.F.Southworth, D.R.

(2023) Nat Commun 14: 3048-3048

  • DOI: https://doi.org/10.1038/s41467-023-38537-y
  • Primary Citation of Related Structures:  
    8FUG

  • PubMed Abstract: 

    Accumulation of filamentous aggregates of tau protein in the brain is a pathological hallmark of Alzheimer's disease (AD) and many other neurodegenerative tauopathies. The filaments adopt disease-specific cross-β amyloid conformations that self-propagate and are implicated in neuronal loss. Development of molecular diagnostics and therapeutics is of critical importance. However, mechanisms of small molecule binding to the amyloid core is poorly understood. We used cryo-electron microscopy to determine a 2.7 Å structure of AD patient-derived tau paired-helical filaments bound to the PET ligand GTP-1. The compound is bound stoichiometrically at a single site along an exposed cleft of each protofilament in a stacked arrangement matching the fibril symmetry. Multiscale modeling reveals pi-pi aromatic interactions that pair favorably with the small molecule-protein contacts, supporting high specificity and affinity for the AD tau conformation. This binding mode offers critical insight into designing compounds to target different amyloid folds found across neurodegenerative diseases.


  • Organizational Affiliation

    Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Microtubule-associated protein tau
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W
73Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P10636 (Homo sapiens)
Explore P10636 
Go to UniProtKB:  P10636
PHAROS:  P10636
GTEx:  ENSG00000186868 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10636
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y9H (Subject of Investigation/LOI)
Query on Y9H

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth E]
CA [auth F]
DA [auth G]
EA [auth H]
AA [auth D],
BA [auth E],
CA [auth F],
DA [auth G],
EA [auth H],
FA [auth I],
GA [auth J],
HA [auth K],
IA [auth L],
JA [auth M],
KA [auth N],
LA [auth O],
MA [auth P],
NA [auth Q],
OA [auth R],
PA [auth S],
QA [auth T],
RA [auth U],
SA [auth V],
TA [auth W],
X [auth A],
Y [auth B],
Z [auth C]
(5S)-2-[4-(2-fluoroethyl)piperidin-1-yl]pyrimido[1,2-a]benzimidazole
C17 H19 F N4
DWSFKWXDRBTTCG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1

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 StatesAG002132
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM139379

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release