7L51 | pdb_00007l51

Solution NMR structure of the dimeric form of the cyclic plant protein PDP-23 in H2O

• PDB DOI: https://doi.org/10.2210/pdb7L51/pdb
• BMRB: 30827

• Classification: PLANT PROTEIN
• Organism(s): Zinnia elegans
• Mutation(s): No 


• Deposited: 2020-12-21 Released: 2021-01-20 
• Deposition Author(s): Payne, C.D., Rosengren, K.J.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

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

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

• PubMed: 34040741 
• DOI: https://doi.org/10.1039/d1sc00692d
• Primary Citation 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.

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Organizational Affiliation: 
• The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia [e-mail].
The University of Western Australia, School of Molecular Sciences, The ARC Centre of Excellence in Plant Energy Biology Crawley WA 6009 Australia.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.27 kDa 
• Atom Count: 438 
• Modeled Residue Count: 56 
• Deposited Residue Count: 56 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic plant protein PDP-23	A, B	28	Zinnia elegans	Mutation(s): 0

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-01-20 
Deposition Author(s): Payne, C.D., Rosengren, K.J.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP190102058

Revision History  

• 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: 2024-10-23
  Changes: Data collection, Database references, Structure summary