9JBL | pdb_00009jbl

Crystal structure of amyloidogenic peptide Bz-FFAALL-NH2

• PDB DOI: https://doi.org/10.2210/pdb9JBL/pdb

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


• Deposited: 2024-08-27 Released: 2025-04-09 
• Deposition Author(s): Sawazaki, T., Murai, F., Yamamoto, K., Sasaki, D., Sohma, Y.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.044 (Depositor), 0.069 (DCC) 
• R-Value Work: 
  0.036 (Depositor), 0.068 (DCC) 
• R-Value Observed: 
  0.037 (Depositor) 

Starting Model: experimental

Literature

Amyloid-reoriented enzyme catalysis.

Sawazaki, T., Murai, F., Yamamoto, K., Sasaki, D., Sohma, Y.

(2025) Nat Commun 16: 3164-3164

• PubMed: 40175427 
• DOI: https://doi.org/10.1038/s41467-025-58536-5
• Primary Citation of Related Structures:  
  9JBL


• PubMed Abstract: 
  

  Enzyme catalysis is essential for molecular transformations. Here, we make use of amyloid, a fibrillar aggregate formed by stacking peptides with β-sheet, which offers unique selectivity in enzymatic reactions. Azo-stilbene derivative (ASB), the amyloid-recognition motif, is incorporated into the substrate, which allows the amyloid consisting of Bz-Phe-Phe-Ala-Ala-Leu-Leu-NH ₂ (BL7) to shield the substrates from the approaching enzyme. X-ray crystallographic analysis and structure-shielding effect relationship studies of BL7 reveal that the benzene rings present in the N-terminal benzoyl group and Phe1 side chain are particularly important for the shielding effect on the substrate. The finding results in a selective transformation system in which the reactive site close to ASB is protected by amyloid, while a site far from ASB is converted by the enzymes (trypsin, protein arginine deiminase [PAD], and Staphylococcus aureus V-8 Protease [Glu-C]). Further, the amyloid-shielded enzyme catalysis is compatible with an intact peptide, as the side chain of Tyr can be converted to the amyloid-recognizing motif. The enzymatic reactions combining amyloid provide unique selectivity for molecular transformation which may be used in diverse fields, including in synthetic chemistry.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama, Japan. [e-mail].
Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama, Japan.
Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 0.78 kDa 
• Atom Count: 57 
• Modeled Residue Count: 7 
• Deposited Residue Count: 7 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloidogenic peptide	A	7	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1L4D	A	L-PEPTIDE LINKING	C16 H15 N O3		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.044 (Depositor), 0.069 (DCC) 
• R-Value Work:  0.036 (Depositor), 0.068 (DCC) 
• R-Value Observed: 0.037 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 4.813	α = 90
b = 32.067	β = 99.24
c = 13.478	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Sawazaki, T., Murai, F., Yamamoto, K., Sasaki, D., Sohma, Y.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121001

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release
  
• Version 1.1: 2025-04-16
  Changes: Database references