45JF | pdb_000045jf

Discovery of Ribosomally Synthesized and Post-translationally Modified Knottin from the Deep-Sea Sponge Stryphnus fortis

• PDB DOI: https://doi.org/10.2210/pdb45JF/pdb

• Classification: RIBOSOMAL PROTEIN
• Organism(s): Stryphnus fortis
• Mutation(s): No 


• Deposited: 2026-08-31 Released: 2026-10-14 
• Deposition Author(s): Daly, N.L., Gunasekera, S.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

Discovery of Ribosomally Synthesized and Post-translationally Modified Knottins from the Deep-Sea Sponge Stryphnus fortis .

Kosgahakumbura, L.N., Slazak, B., Daly, N.L., Fadoul, R., Mohamed, S., Jacobsson, E., Xiong, R., Hellman, B., Goransson, U., Hettiarachchi, C.M., Cardenas, P., Gunasekera, S.

(2026) J Nat Prod 89: 2118-2132

• PubMed: 42261690 
• DOI: https://doi.org/10.1021/acs.jnatprod.6c00501
• Primary Citation Related Structures: 
  45JF


• PubMed Abstract: 
  

  Knottins are stable, structurally constrained mini-proteins with diverse bioactivities. This work presents the first report of a novel family of knottins, 'stryphnines', from the deep-sea sponge Stryphnus fortis. Peptidomic and transcriptomic analysis revealed a rich peptide repertoire and confirmed their ribosomal and sponge origin. This led to the isolation of two novel knottins containing a side-chain to side-chain ester linkage between serine 10/11 and glutamic acid 29/30, respectively, alongside one of their counterpart peptides devoid of the ester bond. The cryptic ester linkage was difficult to resolve due to β-elimination occurring at the serine side-chain ester. However, a combination of NMR, pH incubation studies, and MS/MS analysis facilitated their complete identification. Both stryphnines with and without the ester linkage exhibited no cytotoxicity and genotoxicity to mammalian cells. In contrast, stryphnines with the ester linkage strongly inhibited biofouling by barnacle larvae Amphibalanus improvisus and inhibited bacterial sialidase from Clostridium perfringens . The core knottin framework remained extremely stable in human serum at physiological conditions, despite ester bond hydrolysis occurring at high temperature and different pH treatments. The positive attributes of nontoxicity and biological stability, alongside demonstrated bioactivities, open up opportunities to further investigate the true ecological role and biosynthetic mechanisms of stryphnines.

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Organizational Affiliation: 
• Pharmacognosy, Department of Pharmaceutical Biosciences, Biomedical Center, Uppsala University, Box 591, SE-751 24 Uppsala, Sweden.
Department of Chemistry, University of Colombo, 00300 Colombo, Sri Lanka.
W. Szafer Institute of Botany, Polish Academy of Science, 46 Lubicz Street, 31-512 Kracow, Poland.
Australian Institute of Tropical Health and Medicine, James Cook University, 4870 Cairns, Queensland, Australia.
Drug Safety and Toxicology, Department of Pharmaceutical Biosciences, Biomedical Center, SE-751 24 Uppsala, Sweden.
SciLifeLab, Department of Chemistry for Life Sciences, Uppsala University, Box 576, SE-75123 Uppsala, Sweden.
Museum of Evolution, Uppsala University, Norbyvägen 16, SE-752 36 Uppsala, Sweden.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 3.36 kDa 
• Atom Count: 230 
• Modeled Residue Count: 32 
• Deposited Residue Count: 32 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stryphnine A	A	32	Stryphnus fortis	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-14 
Deposition Author(s): Daly, N.L., Gunasekera, S.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2017-05416

Revision History  

• Version 1.0: 2026-10-14
  Type: Initial release
  
• Version 1.1: 2026-10-21
  Changes: Database references