8OT3 | pdb_00008ot3

unseeded Abeta(1-40) amyloid fibril (morphology ii)

• PDB DOI: https://doi.org/10.2210/pdb8OT3/pdb
• EM Map EMD-17167: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-20 Released: 2024-02-07 
• Deposition Author(s): Pfeiffer, P.B., Schmidt, M., Faendrich, M.
• Funding Organization(s): German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.73 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Literature

Cryo-EM Analysis of the Effect of Seeding with Brain-derived A beta Amyloid Fibrils.

Pfeiffer, P.B., Ugrina, M., Schwierz, N., Sigurdson, C.J., Schmidt, M., Fandrich, M.

(2023) J Mol Biology 436: 168422-168422

• PubMed: 38158175 
• DOI: https://doi.org/10.1016/j.jmb.2023.168422
• Primary Citation Related Structures: 
  8OT1, 8OT3, 8OT4


• PubMed Abstract: 
  

  Aβ amyloid fibrils from Alzheimer's brain tissue are polymorphic and structurally different from typical in vitro formed Aβ fibrils. Here, we show that brain-derived (ex vivo) fibril structures can be proliferated by seeding in vitro. The proliferation reaction is only efficient for one of the three abundant ex vivo Aβ fibril morphologies, which consists of two peptide stacks, while the inefficiently proliferated fibril morphologies contain four or six peptide stacks. In addition to the seeded fibril structures, we find that de novo nucleated fibril structures can emerge in seeded samples if the seeding reaction is continued over multiple generations. These data imply a competition between de novo nucleation and seed extension and suggest further that seeding favours the outgrowth of fibril morphologies that contain fewer peptide stacks.

---

Organizational Affiliation: 
• Institute of Protein Biochemistry, Ulm University, Helmholtzstraße 8/1, 89081 Ulm, Germany. Electronic address: [e-mail].
Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany.
Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0612, USA.
Institute of Protein Biochemistry, Ulm University, Helmholtzstraße 8/1, 89081 Ulm, Germany.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 52.03 kDa 
• Atom Count: 2,460 
• Modeled Residue Count: 336 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid-beta A4 protein	A, B, C, D, E, F, G, H, I, J, K, L	40	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
PHAROS:  P05067 GTEx:  ENSG00000142192

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.73 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1-4487
RECONSTRUCTION	RELION	3.1.3

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Pfeiffer, P.B., Schmidt, M., Faendrich, M.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	FA 456/24-1

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release