7QHI
Crystal structure of cytotoxin 13 from Naja naja, hexagonal form
This is a non-PDB format compatible entry.
Summary for 7QHI
| Entry DOI | 10.2210/pdb7qhi/pdb |
| Descriptor | Cytotoxin 13 (2 entities in total) |
| Functional Keywords | three-finger toxin, cobra snake venom, s-ttpe cytotoxin, toxin |
| Biological source | Naja naja (Indian cobra) |
| Total number of polymer chains | 3 |
| Total formula weight | 20268.82 |
| Authors | Samygina, V.R.,Dubova, K.M.,Bourenkov, G.,Utkin, Y.N.,Dubovskii, P.V. (deposition date: 2021-12-12, release date: 2022-04-27, Last modification date: 2024-10-23) |
| Primary citation | Dubovskii, P.V.,Dubova, K.M.,Bourenkov, G.,Starkov, V.G.,Konshina, A.G.,Efremov, R.G.,Utkin, Y.N.,Samygina, V.R. Variability in the Spatial Structure of the Central Loop in Cobra Cytotoxins Revealed by X-ray Analysis and Molecular Modeling. Toxins, 14:-, 2022 Cited by PubMed Abstract: Cobra cytotoxins (CTs) belong to the three-fingered protein family and possess membrane activity. Here, we studied cytotoxin 13 from cobra venom (CT13Nn). For the first time, a spatial model of CT13Nn with both "water" and "membrane" conformations of the central loop (loop-2) were determined by X-ray crystallography. The "water" conformation of the loop was frequently observed. It was similar to the structure of loop-2 of numerous CTs, determined by either NMR spectroscopy in aqueous solution, or the X-ray method. The "membrane" conformation is rare one and, to date has only been observed by NMR for a single cytotoxin 1 from (CT1No) in detergent micelle. Both CT13Nn and CT1No are S-type CTs. Membrane-binding of these CTs probably involves an additional step-the conformational transformation of the loop-2. To confirm this suggestion, we conducted molecular dynamics simulations of both CT1No and CT13Nn in the Highly Mimetic Membrane Model of palmitoiloleoylphosphatidylglycerol, starting with their "water" NMR models. We found that the both toxins transform their "water" conformation of loop-2 into the "membrane" one during the insertion process. This supports the hypothesis that the S-type CTs, unlike their P-type counterparts, require conformational adaptation of loop-2 during interaction with lipid membranes. PubMed: 35202176DOI: 10.3390/toxins14020149 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.302 Å) |
Structure validation
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