5Y0J | pdb_00005y0j

Solution structure of arenicin-3 derivative N2


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 5Y0J

This is version 1.3 of the entry. See complete history

Literature

Antibacterial and detoxifying activity of NZ17074 analogues with multi-layers of selective antimicrobial actions against Escherichia coli and Salmonella enteritidis

Yang, N.Liu, X.Teng, D.Li, Z.Wang, X.Mao, R.Wang, X.M.Hao, Y.Wang, J.

(2017) Sci Rep 7: 3392-3392

  • DOI: https://doi.org/10.1038/s41598-017-03664-2
  • Primary Citation Related Structures: 
    5Y0H, 5Y0I, 5Y0J

  • PubMed Abstract: 

    NZ17074 (N1), an arenicin-3 derivative isolated from the lugworm, has potent antibacterial activity and is cytotoxic. To reduce its cytotoxicity, seven N1 analogues with different structures were designed by changing their disulfide bonds, hydrophobicity, or charge. The "rocket" analogue-N2 and the "kite" analogue-N6 have potent activity and showed lower cytotoxicity in RAW264.7 cells than N1. The NMR spectra revealed that N1, N2, and N6 adopt β-sheet structures stabilized by one or two disulfide bonds. N2 and N6 permeabilized the outer/inner membranes of E. coli, but did not permeabilize the inner membranes of S. enteritidis. N2 and N6 induced E. coli and S. enteritidis cell cycle arrest in the I-phase and R-phase, respectively. In E. coli and in S. enteritidis, 18.7-43.8% of DNA/RNA/cell wall synthesis and 5.7-61.8% of DNA/RNA/protein synthesis were inhibited by the two peptides, respectively. Collapsed and filamentous E. coli cells and intact morphologies of S. enteritidis cells were observed after treatment with the two peptides. Body weight doses from 2.5-7.5 mg/kg of N2 and N6 enhanced the survival rate of peritonitis- and endotoxemia-induced mice; reduced the serum IL-6, IL-1β and TNF-α levels; and protected mice from lipopolysaccharide-induced lung injury. These data indicate that N2 and N6, through multiple selective actions, may be promising dual-function candidates as novel antimicrobial and anti-endotoxin peptides.


  • Organizational Affiliation
    • Key Laboratory of Feed Biotechnology, Ministry of Agriculture, Beijing, 100081, China.

Macromolecule Content 

  • Total Structure Weight: 2.58 kDa 
  • Atom Count: 178 
  • 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
N221Arenicola marinaMutation(s): 0 

Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China31372346

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2018-03-14
    Changes: Experimental preparation
  • Version 1.2: 2023-06-14
    Changes: Database references, Derived calculations, Other
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Structure summary