5M9U | pdb_00005m9u

Spatial structure of antimicrobial peptide arenicin-1 mutant V8R


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Dimerization of the antimicrobial peptide arenicin plays a key role in the cytotoxicity but not in the antibacterial activity.

Panteleev, P.V.Myshkin, M.Y.Shenkarev, Z.O.Ovchinnikova, T.V.

(2017) Biochem Biophys Res Commun 482: 1320-1326

  • DOI: https://doi.org/10.1016/j.bbrc.2016.12.035
  • Primary Citation Related Structures: 
    5M9U

  • PubMed Abstract: 

    The β-hairpin antimicrobial peptides arenicins from marine polychaeta Arenicola marina exhibit a broad spectrum of antimicrobial activity and high cytotoxicity. In this study the biological activities of arenicin-1 and its therapeutically valuable analog Ar-1[V8R] were investigated. The peptide Ar-1[V8R] displays significantly reduced cytotoxicity against mammalian cells relative to the wild-type arenicin-1. At the same time, both peptides exhibit similar antibacterial activities and kinetics of bacterial membrane permeabilization. Comparative NMR analysis of the peptides spatial structures in water and membrane-mimicking environment showed that Ar-1[V8R] in contrast to arenicin has significantly lower dimerization propensity. Thus, dimerization of the antimicrobial peptide arenicin plays a key role in the cytotoxicity but not in the antibacterial activity.


  • Organizational Affiliation
    • M.M.Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow, Russia.

Macromolecule Content 

  • Total Structure Weight: 2.82 kDa 
  • Atom Count: 198 
  • Modeled Residue Count: 21 
  • Deposited Residue Count: 21 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Arenicin-121Arenicola marinaMutation(s): 1 
UniProt
Find proteins for Q5SC60 (Arenicola marina)
Explore Q5SC60 
Go to UniProtKB:  Q5SC60
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SC60
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Structure summary