2G9L | pdb_00002g9l

The High-resolution Solution Conformation of an Antimicrobial Peptide Gaegurin 4 and Its Mode of Membrane Interaction

• PDB DOI: https://doi.org/10.2210/pdb2G9L/pdb
• BMRB: 7065

• Classification: ANTIBIOTIC
• Organism(s): Glandirana rugosa
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2006-03-06 Released: 2007-01-16 
• Deposition Author(s): Chi, S.-W., Han, K.-H.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure and membrane interaction mode of an antimicrobial peptide gaegurin 4

Chi, S.-W., Kim, J.-S., Kim, D.-H., Lee, S.-H., Park, Y.-H., Han, K.-H.

(2007) Biochem Biophys Res Commun 352: 592-597

• PubMed: 17141187 
• DOI: https://doi.org/10.1016/j.bbrc.2006.11.064
• Primary Citation Related Structures: 
  2G9L


• PubMed Abstract: 
  

  We have applied NMR spectroscopy to determine the high-resolution structure of gaegurin 4, a 37-residue antimicrobial peptide from Rana rugosa, under varying hydrophobic conditions. Even in 100% H2O, gaegurin 4 contains a nascent turn near its C-terminal Rana box. Under a more hydrophobic condition it forms two amphipathic helices, one long encompassing residues 2-23 and the other consisting of residues 25-34, similar to what has been observed in cecropin A. Functional implication of the helix-breaking kink at Gly24 in gaegurin 4 was investigated by preparing several analogs. Based upon the current and previous results, we propose a novel seaanemone-like ion pore-forming model for gaegurin 4.

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Organizational Affiliation: 
• Molecular Cancer Research Center, Division of Molecular Therapeutics, KRIBB, Daejeon 305-806, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.76 kDa 
• Atom Count: 261 
• Modeled Residue Count: 37 
• Deposited Residue Count: 37 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gaegurin-4	A	37	N/A	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P80398 (Glandirana rugosa) Explore P80398  Go to UniProtKB:  P80398

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-16 
Deposition Author(s): Chi, S.-W., Han, K.-H.

Revision History  

• Version 1.0: 2007-01-16
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-09
  Changes: Data collection, Database references, Derived calculations, Experimental preparation
• Version 1.4: 2024-10-23
  Changes: Data collection, Structure summary