6FHC

Crystal Structure of the Amyloid-like hexametric polymorph of the LFKFFK segment from the S. aureus PSMalpha3

  • Classification: PROTEIN FIBRIL
  • Organism(s): Staphylococcus aureus
  • Mutation(s): No 

  • Deposited: 2018-01-14 Released: 2018-08-08 
  • Deposition Author(s): Landau, M., Colletier, J.-P.
  • Funding Organization(s): Israel Science Foundation, Deutsch-IsraelischeProjektkooperation (DIP), I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation, United States - Israel Binational Science Foundation (BSF)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.122 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Extreme amyloid polymorphism in Staphylococcus aureus virulent PSM alpha peptides.

Salinas, N.Colletier, J.P.Moshe, A.Landau, M.

(2018) Nat Commun 9: 3512-3512

  • DOI: https://doi.org/10.1038/s41467-018-05490-0
  • Primary Citation of Related Structures:  
    6FG4, 6FGR, 6FHC, 6FHD

  • PubMed Abstract: 

    Members of the Staphylococcus aureus phenol-soluble modulin (PSM) peptide family are secreted as functional amyloids that serve diverse roles in pathogenicity and may be present as full-length peptides or as naturally occurring truncations. We recently showed that the activity of PSMα3, the most toxic member, stems from the formation of cross-α fibrils, which are at variance with the cross-β fibrils linked with eukaryotic amyloid pathologies. Here, we show that PSMα1 and PSMα4, involved in biofilm structuring, form canonical cross-β amyloid fibrils wherein β-sheets tightly mate through steric zipper interfaces, conferring high stability. Contrastingly, a truncated PSMα3 has antibacterial activity, forms reversible fibrils, and reveals two polymorphic and atypical β-rich fibril architectures. These architectures are radically different from both the cross-α fibrils formed by full-length PSMα3, and from the canonical cross-β fibrils. Our results point to structural plasticity being at the basis of the functional diversity exhibited by S. aureus PSMαs.


  • Organizational Affiliation

    Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Psm alpha-36Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for H9BRQ7 (Staphylococcus aureus)
Explore H9BRQ7 
Go to UniProtKB:  H9BRQ7
Entity Groups  
UniProt GroupH9BRQ7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
D [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
CO3
Query on CO3

Download Ideal Coordinates CCD File 
B [auth A]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
SCN
Query on SCN

Download Ideal Coordinates CCD File 
C [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.122 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.791α = 90
b = 35.791β = 90
c = 9.632γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael560/16
Deutsch-IsraelischeProjektkooperation (DIP)Israel3655/1-1
I-CORE Program of the Planning and Budgeting Committee and The Israel Science FoundationIsrael1775/12
United States - Israel Binational Science Foundation (BSF)Israel2013254

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.2: 2022-03-30
    Changes: Author supporting evidence, Database references