7YAT

CryoEM tetra protofilament structure of the hamster prion 108-144 fibril

• PDB DOI: https://doi.org/10.2210/pdb7YAT/pdb
• EM Map EMD-33719: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Mesocricetus auratus
• Mutation(s): No 


• Deposited: 2022-06-28 Released: 2022-07-27 
• Deposition Author(s): Chen, E.H.-L., Kao, S.-W., Lee, C.-H., Huang, J.Y.C., Chen, R.P.-Y., Wu, K.-P.
• Funding Organization(s): Academia Sinica (Taiwan), Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.20 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

2.2 angstrom Cryo-EM Tetra-Protofilament Structure of the Hamster Prion 108-144 Fibril Reveals an Ordered Water Channel in the Center.

Chen, E.H., Kao, H.W., Lee, C.H., Huang, J.Y.C., Wu, K.P., Chen, R.P.

(2022) J Am Chem Soc 144: 13888-13894

• PubMed: 35857020 
• DOI: https://doi.org/10.1021/jacs.2c05479
• Primary Citation of Related Structures:  
  7YAT


• PubMed Abstract: 
  

  Fibrils of the hamster prion peptide (sHaPrP, sequence 108-144) were prepared in an acidic solution, and their structure was solved by cryogenic electron microscopy with a resolution of 2.23 Å based on the gold-standard Fourier shell correlation (FSC) curve. The fibril has a novel architecture that has never been found in other amyloid fibrils. Each fibril is assembled by four protofilaments (PFs) and has an ordered water channel in the center. Each protofilament contains three β-strands (125-130, 133-135, and 138-141) arranged in an "R"-shaped construct. The structural data indicate that these three β-strand segments are the most amyloidogenic region of the prion peptide/protein and might be the site of nucleation during fibrillization under conditions without denaturants.

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Organizational Affiliation: 

Institute of Biological Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Nankang, Taipei 115, Taiwan.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 60 kDa 
• Atom Count: 4,129 
• Modelled Residue Count: 600 
• Deposited Residue Count: 600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major prion protein	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W [auth X], X [auth Y]	25	Mesocricetus auratus	Mutation(s): 0
UniProt
Find proteins for P04273 (Mesocricetus auratus) Explore P04273  Go to UniProtKB:  P04273

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.20 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): Chen, E.H.-L., Kao, S.-W., Lee, C.-H., Huang, J.Y.C., Chen, R.P.-Y., Wu, K.-P.

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Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	AS-CDA-110-L03
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	MOST 105-2119-M-001-028
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	106-2923-M-001-003-MY3
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	109-2113-M-001-001
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	MOST 109-2311-B-001-022

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2022-08-03
  Changes: Database references
• Version 1.2: 2022-08-17
  Changes: Database references