Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Predict Membrane 

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3.21 kDa 
• Atom Count: 224 
• Modelled Residue Count: 26 
• Deposited Residue Count: 26 
• Unique protein chains: 1

2PCO

Spatial Structure and Membrane Permeabilization for Latarcin-1, a Spider Antimicrobial Peptide

• PDB DOI: 10.2210/pdb2PCO/pdb
• BMRB: 7402

• Classification: TOXIN
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2007-03-30 Released: 2008-03-18 
• Deposition Author(s): Dubovskii, P.V., Volynsky, P.E., Polyansky, A.A., Chupin, V.V., Efremov, R.G., Arseniev, A.S.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Three-dimensional structure/hydrophobicity of latarcins specifies their mode of membrane activity.

Dubovskii, P.V., Volynsky, P.E., Polyansky, A.A., Karpunin, D.V., Chupin, V.V., Efremov, R.G., Arseniev, A.S.

(2008) Biochemistry 47: 3525-3533

• PubMed: 18293934 
• DOI: 10.1021/bi702203w
• Primary Citation of Related Structures:  
  2PCO


• PubMed Abstract: 
  

Latarcins, linear peptides from the Lachesana tarabaevi spider venom, exhibit a broad-spectrum antimicrobial activity, likely acting on the bacterial cytoplasmic membrane. We study their spatial structures and interaction with model membranes by a combination of experimental and theoretical methods to reveal the structure-activity relationship. In this work, a 26 amino acid peptide, Ltc1, was investigated. Its spatial structure in detergent micelles was determined by (1)H nuclear magnetic resonance (NMR) and refined by Monte Carlo simulations in an implicit water-octanol slab. The Ltc1 molecule was found to form a straight uninterrupted amphiphilic helix comprising 8-23 residues. A dye-leakage fluorescent assay and (31)P NMR spectroscopy established that the peptide does not induce the release of fluorescent marker nor deteriorate the bilayer structure of the membranes. The voltage-clamp technique showed that Ltc1 induces the current fluctuations through planar membranes when the sign of the applied potential coincides with the one across the bacterial inner membrane. This implies that Ltc1 acts on the membranes via a specific mechanism, which is different from the carpet mode demonstrated by another latarcin, Ltc2a, featuring a helix-hinge-helix structure with a hydrophobicity gradient along the peptide chain. In contrast, the hydrophobic surface of the Ltc1 helix is narrow-shaped and extends with no gradient along the axis. We have also disclosed a number of peptides, structurally homologous to Ltc1 and exhibiting similar membrane activity. This indicates that the hydrophobic pattern of the Ltc1 helix and related antimicrobial peptides specifies their activity mechanism. The latter assumes the formation of variable-sized lesions, which depend upon the potential across the membrane.

---

Organizational Affiliation: 

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya Str., Moscow 117997, Russia. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Latarcin-1	A	26	N/A	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q1ELT9 (Lachesana tarabaevi) Explore Q1ELT9  Go to UniProtKB:  Q1ELT9

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: target function 
• OLDERADO: 2PCO Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-03-30 
• Released Date: 2008-03-18 
Deposition Author(s): Dubovskii, P.V., Volynsky, P.E., Polyansky, A.A., Chupin, V.V., Efremov, R.G., Arseniev, A.S.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations