9GJ3 | pdb_00009gj3

Structure of the amyloid-forming peptide LYIQNY

  • Classification: PROTEIN FIBRIL
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2024-08-21 Released: 2025-07-09 
  • Deposition Author(s): Durvanger, Z.
  • Funding Organization(s): Hungarian National Research, Development and Innovation Office, European Regional Development Fund

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.110 (Depositor), 0.110 (DCC) 
  • R-Value Work: 
    0.100 (Depositor), 0.100 (DCC) 
  • R-Value Observed: 
    0.101 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9GJ3

This is version 1.0 of the entry. See complete history

Literature

Chemical Evolution of Early Macromolecules: From Prebiotic Oligopeptides to Self-Organizing Biosystems via Amyloid Formation.

Bencs, F.Taricska, N.Durvanger, Z.Horvath, D.Fazekas, Z.Grolmusz, V.Farkas, V.Perczel, A.

(2025) Chemistry 31: e202404669-e202404669

  • DOI: https://doi.org/10.1002/chem.202404669
  • Primary Citation Related Structures: 
    9GJ3, 9GJ4

  • PubMed Abstract: 

    Short amyloidogenic oligopeptides (APRs) are proposed as early macromolecules capable of forming solvent-separated nanosystems under prebiotic conditions. This study provides experimental evidence that APRs, such as the aggregation-prone oligopeptide A (APR-A), can undergo mutational transitions to form distinct variants and convert to APR-B, either amyloid-like or water-soluble and non-aggregating. These transitions occur along a spectrum from strongly amyloidogenic (pro-amyloid) to weakly amyloidogenic (anti-amyloid), with the mutation sequence order playing a key role in determining their physicochemical properties. The pro-amyloid pathway facilitates heterogeneous phase separation, leading to amyloid-crystal formation with multiple polymorphs, including the first class 3 amyloid topology. By mapping these transitions, we demonstrate the potential co-evolution of water-soluble miniproteins and insoluble amyloids, both of which could have been pivotal in early bio-nanosystem formation. These insights into amyloid modulation provide a crucial step toward understanding amyloid control mechanisms.


  • Organizational Affiliation
    • ELTE Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary.

Macromolecule Content 

  • Total Structure Weight: 0.81 kDa 
  • Atom Count: 58 
  • Modeled Residue Count: 6 
  • Deposited Residue Count: 6 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptide LYIQNY6synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.110 (Depositor), 0.110 (DCC) 
  • R-Value Work:  0.100 (Depositor), 0.100 (DCC) 
  • R-Value Observed: 0.101 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 4.85α = 90
b = 20.538β = 90
c = 42.326γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
BUSTERrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Hungarian National Research, Development and Innovation OfficeHungary2018-1.2.1-NKP-2018-00005
European Regional Development FundEuropean UnionVEKOP-2.3.2-16-2017-00014, VEKOP-2.3.3-15-2017-00018
Hungarian National Research, Development and Innovation OfficeHungaryThematic Excellence Program Synth+

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release