5MOU | pdb_00005mou

NMR spatial structure of scorpion alpha-like toxin BeM9

• PDB DOI: https://doi.org/10.2210/pdb5MOU/pdb
• BMRB: 34078

• Classification: PROTEIN
• Organism(s): Mesobuthus eupeus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-14 Released: 2018-01-17 
• Deposition Author(s): Mineev, K.S., Kuldushev, N.A., Berkut, A.A., Grishin, E.V., Vassilevski, A.A., Arseniev, A.S.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Literature

Refined structure of BeM9 reveals arginine hand, an overlooked structural motif in scorpion toxins affecting sodium channels.

Kuldyushev, N.A., Mineev, K.S., Berkut, A.A., Peigneur, S., Arseniev, A.S., Tytgat, J., Grishin, E.V., Vassilevski, A.A.

(2018) Proteins 86: 1117-1122

• PubMed: 30007037 
• DOI: https://doi.org/10.1002/prot.25583
• Primary Citation of Related Structures:  
  5MOU


• PubMed Abstract: 
  

  Sodium channel alpha-toxins from scorpion venom (α-NaTx) inhibit the inactivation of voltage-gated sodium channels. We used solution NMR to investigate the structure of BeM9 toxin from Mesobuthus eupeus scorpion, a prototype α-NaTx classified as an "α-like" toxin due to its wide spectrum of activity on insect and mammalian channels. We identified a new motif that we named "arginine hand," whereby arginine side chain forms several hydrogen bonds with main chain atoms. The arginine hand was found in the "specificity module," a part of the molecule that dictates toxin selectivity; and just single arginine-to-lysine point mutation drastically changed BeM9 selectivity profile.

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Organizational Affiliation: 

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 7.35 kDa 
• Atom Count: 510 
• Modelled Residue Count: 66 
• Deposited Residue Count: 66 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-mammal toxin BeM9	A	66	Mesobuthus eupeus	Mutation(s): 0
UniProt
Find proteins for P09981 (Mesobuthus eupeus) Explore P09981  Go to UniProtKB:  P09981

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Mineev, K.S., Kuldushev, N.A., Berkut, A.A., Grishin, E.V., Vassilevski, A.A., Arseniev, A.S.

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2018-08-29
  Changes: Data collection, Database references
• Version 1.2: 2018-11-28
  Changes: Data collection, Database references
• Version 1.3: 2019-02-20
  Changes: Data collection, Structure summary
• Version 1.4: 2019-05-08
  Changes: Data collection
• Version 1.5: 2024-11-13
  Changes: Data collection, Database references, Structure summary