2N86 | pdb_00002n86

NMR structure of OtTx1a - ICK

• PDB DOI: https://doi.org/10.2210/pdb2N86/pdb
• BMRB: 25836

• Classification: TOXIN
• Organism(s): Oxyopes takobius
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2015-10-05 Released: 2016-10-19 
• Deposition Author(s): Nadezhdin, K., Romanovskaya, D., Sachkova, M., Vassilevski, A., Grishin, E., Kovalchuk, S., Arseniev, A.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Modular toxin from the lynx spider Oxyopes takobius: Structure of spiderine domains in solution and membrane-mimicking environment.

Nadezhdin, K.D., Romanovskaia, D.D., Sachkova, M.Y., Oparin, P.B., Kovalchuk, S.I., Grishin, E.V., Arseniev, A.S., Vassilevski, A.A.

(2017) Protein Sci 26: 611-616

• PubMed: 27997708 
• DOI: https://doi.org/10.1002/pro.3101
• Primary Citation Related Structures: 
  2N85, 2N86


• PubMed Abstract: 
  

  We have recently demonstrated that a common phenomenon in evolution of spider venom composition is the emergence of so-called modular toxins consisting of two domains, each corresponding to a "usual" single-domain toxin. In this article, we describe the structure of two domains that build up a modular toxin named spiderine or OtTx1a from the venom of Oxyopes takobius. Both domains were investigated by solution NMR in water and detergent micelles used to mimic membrane environment. The N-terminal spiderine domain OtTx1a-AMP (41 amino acid residues) contains no cysteines. It is disordered in aqueous solution but in micelles, it assumes a stable amphiphilic structure consisting of two α-helices separated by a flexible linker. On the contrary, the C-terminal domain OtTx1a-ICK (59 residues) is a disulfide-rich polypeptide reticulated by five S-S bridges. It presents a stable structure in water and its core is the inhibitor cystine knot (ICK) or knottin motif that is common among single-domain neurotoxins. OtTx1a-ICK structure is the first knottin with five disulfide bridges and it represents a good reference for the whole oxytoxin family. The affinity of both domains to membranes was measured with NMR using titration by liposome suspensions. In agreement with biological tests, OtTx1a-AMP was found to show high membrane affinity explaining its potent antimicrobial properties.

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Organizational Affiliation: 
• M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia.
Moscow Institute of Physics and Technology (State University), 9 Institutskiy per, Dolgoprudny, Moscow Region, 141700, Russia.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.37 kDa 
• Atom Count: 437 
• Modeled Residue Count: 59 
• Deposited Residue Count: 59 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spiderine-1a	A	59	Oxyopes takobius	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P86716 (Oxyopes takobius) Explore P86716  Go to UniProtKB:  P86716

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Nadezhdin, K., Romanovskaya, D., Sachkova, M., Vassilevski, A., Grishin, E., Kovalchuk, S., Arseniev, A.

Revision History  

• Version 1.0: 2016-10-19
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary