6SIG | pdb_00006sig

Epidermicin antimicrobial protein from Staphylococcus epidermidis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.175 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6SIG

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Flowering Poration-A Synergistic Multi-Mode Antibacterial Mechanism by a Bacteriocin Fold.

Hammond, K.Lewis, H.Halliwell, S.Desriac, F.Nardone, B.Ravi, J.Hoogenboom, B.W.Upton, M.Derrick, J.P.Ryadnov, M.G.

(2020) iScience 23: 101423-101423

  • DOI: https://doi.org/10.1016/j.isci.2020.101423
  • Primary Citation Related Structures: 
    6SIF, 6SIG

  • PubMed Abstract: 

    Bacteriocins are a distinct family of antimicrobial proteins postulated to porate bacterial membranes. However, direct experimental evidence of pore formation by these proteins is lacking. Here we report a multi-mode poration mechanism induced by four-helix bacteriocins, epidermicin NI01 and aureocin A53. Using a combination of crystallography, spectroscopy, bioassays, and nanoscale imaging, we established that individual two-helix segments of epidermicin retain antibacterial activity but each of these segments adopts a particular poration mode. In the intact protein these segments act synergistically to balance out antibacterial and hemolytic activities. The study sets a precedent of multi-mode membrane disruption advancing the current understanding of structure-activity relationships in pore-forming proteins.


  • Organizational Affiliation
    • National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK; London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; Department of Physics & Astronomy, University College London, London WC1E 6BT, UK.

Macromolecule Content 

  • Total Structure Weight: 24.41 kDa 
  • Atom Count: 1,945 
  • Modeled Residue Count: 201 
  • Deposited Residue Count: 204 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Epidermicin locus structural protein
A, B, C, D
51Staphylococcus epidermidisMutation(s): 0 
UniProt
Find proteins for H9BG66 (Staphylococcus epidermidis)
Explore H9BG66 
Go to UniProtKB:  H9BG66
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH9BG66
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.175 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.74α = 90
b = 99.44β = 90
c = 69.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J021474/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references
  • Version 1.2: 2021-03-31
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description