9D70 | pdb_00009d70

Cryo-EM of helical fibers formed by two peptides Pyn-K6 and Pyn-(EY)3

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

  • Deposited: 2024-08-16 Released: 2025-01-22 
  • Deposition Author(s): Zia, A., Qiao, Y., Xu, B., Wang, F.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Context-Dependent Heterotypic Assemblies of Intrinsically Disordered Peptides.

Qiao, Y.Zia, A.Wu, G.Liu, Z.Guo, J.Chu, M.He, H.Wang, F.Xu, B.

(2025) J Am Chem Soc 147: 2978-2983

  • DOI: https://doi.org/10.1021/jacs.4c12150
  • Primary Citation of Related Structures:  
    9D70

  • PubMed Abstract: 

    Despite their critical role in context-dependent interactions for protein functions, intrinsically disordered regions (IDRs) are often overlooked for designing peptide assemblies. Here, we exploit IDRs to enable context-dependent heterotypic assemblies of intrinsically disordered peptides, where "context-dependent" refers to assembly behavior driven by interactions with other molecules. By attaching an aromatic segment to oppositely charged intrinsically disordered peptides, we achieve a nanofiber formation. Although the same-charged peptides cannot self-assemble, oppositely charged peptides form heterotypic nanofibers. Cryo-EM analysis reveals a β-sheet arrangement within the ordered core of these nanofibers, conformational heterogeneity, and a disorder-to-order continuum and shows a high number of hydrogen bonds between tyrosine and lysine ε-amine. Additionally, this work demonstrates a post-assembly morphological change resulting from local conformational flexibility. While equal molar mixtures of the charged intrinsically disordered peptides yield nanofibers, doubling the positively charged peptides after assembly produces bundles of nanofibers. Furthermore, reducing the number of aromatic amino acid residues reduces bundle formation. Demonstrating context-dependent self-assembly of intrinsically disordered peptides and revealing atomistic insights into heterotypic assemblies of intrinsically disordered peptides for the first time, this work illustrates a straightforward approach to enable heterotypic intrinsically disordered peptides to self-assemble for the design of adaptive, multifunctional peptide nanomaterials.


  • Organizational Affiliation
    • Department of Chemistry, Brandeis University, 415 South St., Waltham, Massachusetts 02454, United States.

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PYR-K6A [auth B]7synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PYR-EY3B [auth C]7synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OG9 (Subject of Investigation/LOI)
Query on OG9

Download Ideal Coordinates CCD File 
C [auth B](pyren-1-yl)acetic acid
C18 H12 O2
SDJCLYBBPUHKCD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM138756
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA142746

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-28
    Changes: Data collection