7L54

Solution NMR structure of the cyclic plant protein PDP-23 in SDS micelles


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A chameleonic macrocyclic peptide with drug delivery applications.

Payne, C.D.Franke, B.Fisher, M.F.Hajiaghaalipour, F.McAleese, C.E.Song, A.Eliasson, C.Zhang, J.Jayasena, A.S.Vadlamani, G.Clark, R.J.Minchin, R.F.Mylne, J.S.Rosengren, K.J.

(2021) Chem Sci 12: 6670-6683

  • DOI: https://doi.org/10.1039/d1sc00692d
  • Primary Citation of Related Structures:  
    7L51, 7L53, 7L54, 7L55

  • PubMed Abstract: 

    Head-to-tail cyclized peptides are intriguing natural products with unusual properties. The PawS-Derived Peptides (PDPs) are ribosomally synthesized as part of precursors for seed storage albumins in species of the daisy family, and are post-translationally excised and cyclized during proteolytic processing. Here we report a PDP twice the typical size and with two disulfide bonds, identified from seeds of Zinnia elegans . In water, synthetic PDP-23 forms a unique dimeric structure in which two monomers containing two β-hairpins cross-clasp and enclose a hydrophobic core, creating a square prism. This dimer can be split by addition of micelles or organic solvent and in monomeric form PDP-23 adopts open or closed V-shapes, exposing different levels of hydrophobicity dependent on conditions. This chameleonic character is unusual for disulfide-rich peptides and engenders PDP-23 with potential for cell delivery and accessing novel targets. We demonstrate this by conjugating a rhodamine dye to PDP-23, creating a stable, cell-penetrating inhibitor of the P-glycoprotein drug efflux pump.


  • Organizational Affiliation

    The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia j.rosengren@uq.edu.au.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic plant protein PDP-2328Zinnia elegansMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP190102058

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Database references, Other
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Structure summary