9BHN | pdb_00009bhn

Solution NMR structure of halichondamide A, a fused bicyclic cysteine knot undecapeptide from the marine sponge Halichondria bowerbanki

• PDB DOI: https://doi.org/10.2210/pdb9BHN/pdb
• BMRB: 31170

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Halichondria bowerbanki
• Mutation(s): No 


• Deposited: 2024-04-21 Released: 2024-08-21 
• Deposition Author(s): Agarwal, V., McShan, A.C., Zhong, W.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Discovery and Folding Dynamics of a Fused Bicyclic Cysteine Knot Undecapeptide from the Marine Sponge Halichondria bowerbanki.

Zhong, W., Olugbami, J.O., Rathakrishnan, P., Mohanty, I., Moore, S.G., Garg, N., Oyelere, A.K., Turner, T.L., McShan, A.C., Agarwal, V.

(2024) J Org Chem 89: 12748-12752

• PubMed: 39189383 
• DOI: https://doi.org/10.1021/acs.joc.4c01104
• Primary Citation of Related Structures:  
  9BHN


• PubMed Abstract: 
  

  We describe the discovery and structure of an undecapeptide natural product from a marine sponge, termed halichondamide A, that is morphed into a fused bicyclic ring topology via two disulfide bonds. Molecular dynamics simulations allow us to posit that the installation of one disulfide bond biases the intermediate peptide conformation and predisposes the formation of the second disulfide bond. The natural product was found to be mildly cytotoxic against liver and breast cancer cell lines.

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Organizational Affiliation: 
• School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.
Department of Biochemistry, University of Ibadan, Ibadan, Oyo 200005, Nigeria.
Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.
Ecology, Evolution, and Marine Biology Department, University of California Santa Barbara, Santa Barbara, California 93106, United States.
School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 1.33 kDa 
• Atom Count: 89 
• Modeled Residue Count: 11 
• Deposited Residue Count: 11 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Halichondamide A	A	11	Halichondria bowerbanki	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-21 
Deposition Author(s): Agarwal, V., McShan, A.C., Zhong, W.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-2238650

Revision History  

• Version 1.0: 2024-08-21
  Type: Initial release
  
• Version 1.1: 2024-09-25
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Structure summary