8GI5

Cryo-EM of self-assembling pyrene peptide with Ca2+

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

  • Deposited: 2023-03-13 Released: 2023-06-14 
  • Deposition Author(s): Rich-New, S.T., Guo, J., 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), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Hierarchical Assembly of Intrinsically Disordered Short Peptides.

Guo, J.Rich-New, S.T.Liu, C.Huang, Y.Tan, W.He, H.Yi, M.Zhang, X.Egelman, E.H.Wang, F.Xu, B.

(2023) Chem 9: 2530-2546

  • DOI: https://doi.org/10.1016/j.chempr.2023.04.023
  • Primary Citation of Related Structures:  
    7UUQ, 8GI5

  • PubMed Abstract: 

    The understanding on how short peptide assemblies transit from disorder to order remains limited due to the lack of atomistic structures. Here we report cryo-EM structure of the nanofibers short intrinsically disordered peptides (IDPs). Upon lowering pH or adding calcium ions, the IDP transitions from individual nanoparticles to nanofibers containing an aromatic core and a disordered periphery comprised of 2 to 5 amino acids. Protonating the phosphate or adding more metal ions further assembles the nanofibers into filament bundles. The assemblies of the IDP analogs with controlled chemistry, such as phosphorylation site, hydrophobic interactions, and sequences indicate that metal ions interact with the flexible periphery of the nanoparticles of the IDPs to form fibrils and enhance the interfibrillar interactions to form filament bundles. Illustrating that an IDP self-assembles from disorder to order, this work offers atomistic molecular insights to understand assemblies of short peptides driven by noncovalent interactions.


  • Organizational Affiliation

    Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrene peptide
A, B, C, D
8synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A, B, C, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report



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 Institute of General Medical Sciences (NIH/NIGMS)United StatesGM122510
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA142746
National Science Foundation (NSF, United States)United StatesDMR-2011846

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Data collection, Database references