5FZV | pdb_00005fzv

High resolution solution NMR structure of the spider venom peptide U3- scytotoxin-Sth1a

• PDB DOI: https://doi.org/10.2210/pdb5FZV/pdb
• BMRB: 26002

• Classification: TOXIN
• Organism(s): Scytodes thoracica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2016-03-15 Released: 2016-06-08 
• Deposition Author(s): Loening, N.M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: TOTAL ENERGY 

Literature

Characterization of Three Venom Peptides from the Spitting Spider Scytodes Thoracica.

Ariki, N.K., Munoz, L.E., Armitage, E.L., Goodstein, F.R., George, K.G., Smith, V.L., Vetter, I., Herzig, V., King, G.F., Loening, N.M.

(2016) PLoS One 11: 56291

• PubMed: 27227898 
• DOI: https://doi.org/10.1371/journal.pone.0156291
• Primary Citation Related Structures: 
  5FZV, 5FZW, 5FZX


• PubMed Abstract: 
  

  We present the solution-state NMR structures and preliminary functional characterizations of three venom peptides identified from the spitting spider Scytodes thoracica. Despite little sequence identity to other venom peptides, structural characterization reveals that these peptides contain an inhibitor cystine knot motif common to many venom peptides. These are the first structures for any peptide or protein from spiders of the Scytodidae family. Many venom peptides target neuronal ion channels or receptors. However, we have not been able to determine the target of these Scytodes peptides so we can only state with certainty the channels and receptors that they do not target.

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Organizational Affiliation: 
• Chemistry Department, Lewis & Clark College, 0615 SW Palatine Hill Road, Portland, OR, 97219, United States of America.
Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 3.46 kDa 
• Atom Count: 235 
• Modeled Residue Count: 32 
• Deposited Residue Count: 32 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Venom peptide U3-SYTX-Sth1a	A	32	Scytodes thoracica	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A0A0V662 (Scytodes thoracica) Explore A0A0A0V662  Go to UniProtKB:  A0A0A0V662

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: TOTAL ENERGY 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-08 
Deposition Author(s): Loening, N.M.

Revision History  

• Version 1.0: 2016-06-08
  Type: Initial release
  
• Version 2.0: 2017-06-14
  Changes: Atomic model, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 2.1: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 2.2: 2024-11-20
  Changes: Data collection, Database references, Structure summary