2E2S

Solution structure of agelenin, an insecticidal peptide from the venom of Agelena opulenta

• PDB DOI: https://doi.org/10.2210/pdb2E2S/pdb

• Classification: TOXIN
• Organism(s): Allagelena opulenta
• Mutation(s): No 


• Deposited: 2006-11-17 Released: 2007-08-07 
• Deposition Author(s): Yamaji, N.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of agelenin, an insecticidal peptide isolated from the spider Agelena opulenta, and its structural similarities to insect-specific calcium channel inhibitors

Yamaji, N., Sugase, K., Nakajima, T., Miki, T., Wakamori, M., Mori, Y., Iwashita, T.

(2007) FEBS Lett 581: 3789-3794

• PubMed: 17644092 
• DOI: https://doi.org/10.1016/j.febslet.2007.06.077
• Primary Citation of Related Structures:  
  2E2S


• PubMed Abstract: 
  

  Agelenin, isolated from the Agelenidae spider Agelena opulenta, is a peptide composed of 35 amino acids. We determined the three-dimensional structure of agelenin using two-dimensional NMR spectroscopy. The structure is composed of a short antiparallel beta-sheet and four beta-turns, which are stabilized by three disulfide bonds. Agelenin has characteristic residues, Phe9, Ser28 and Arg33, which are arranged similarly to the pharmacophore of the insect channel inhibitor, omega-atracotoxin-Hv1a. These observations suggest that agelenin and omega-atracotoxin-Hv1a bind to insect calcium channels in a similar manner. We also suggest that another mode of action may operate in the channel inhibition by omega-agatoxin-IVA and omega-atracotoxin-Hv2a.

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Organizational Affiliation: 

Suntory Institute for Bioorganic Research, 1-1-1 Wakayamadai, Shimamoto-Cho, Mishima-Gun, Osaka 618-8503, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3.83 kDa 
• Atom Count: 263 
• Modelled Residue Count: 36 
• Deposited Residue Count: 36 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agelenin	A	36	Allagelena opulenta	Mutation(s): 0
UniProt
Find proteins for P31328 (Allagelena opulenta) Explore P31328  Go to UniProtKB:  P31328

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-07 
Deposition Author(s): Yamaji, N.

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-09
  Changes: Data collection, Database references, Derived calculations