6RC7

NMR structure of cytotoxin 3 from Naja kaouthia in solution, major form

Summary for 6RC7

• Entry DOI: 10.2210/pdb6rc7/pdb
• NMR Information: BMRB: 34392
• Descriptor: Cytotoxin 3 (1 entity in total)
• Functional Keywords: three-finger toxin, cobra snake venom, beta-structure, cytolytic peptide, disulfide-rich protein, toxin
• Biological source: Naja kaouthia (Monocled cobra)
• Total number of polymer chains: 1
• Total formula weight: 6728.22

Authors

Dubinnyi, M.A.,Dubovskii, P.V.,Utkin, Y.N.,Arseniev, A.S. (deposition date: 2019-04-11, release date: 2020-05-13, Last modification date: 2024-10-09)

Primary citation

Dubinnyi, M.A.,Dubovskii, P.V.,Starkov, V.G.,Utkin, Y.N.
The omega-loop of cobra cytotoxins tolerates multiple amino acid substitutions.
Biochem.Biophys.Res.Commun., 558:141-146, 2021

PubMed Abstract: Cobra cytotoxins (CTs), the three-fingered proteins, feature high amino acid sequence homology in the beta-strands and variations in the loop regions. We selected a pair of cytotoxins from Naja kaouthia crude venom to clarify the sequence-structure relationships. Using chromatography and mass spectroscopy, we separated and identified the mixture of cytotoxins 2 and 3, differentiated by the only Val 41/Ala 41 substitution. Here, using natural abundance C, N NMR-spectroscopy we performed chemical shift assignments of the signals of the both toxins in aqueous solution in the major and minor forms. Combining NOE and chemical shift data, the toxins' spatial structure was determined. Finally, we proved that the tip of the "finger"-2, or the loop-2 of cytotoxins adopts the shape of an omega-loop with a tightly-bound water molecule in its cavity. Comparison with other NMR and X-ray structures of cytotoxins possessing different amino acid sequences reveals spatial similarity in this family of proteins, including the loop-2 region, previously considered to be flexible.

PubMed: 33915327
DOI: 10.1016/j.bbrc.2021.04.069

Experimental method

SOLUTION NMR