5I55

Crystal Structure of the Virulent PSM-alpha3 Peptide Forming a Cross-alpha amyloid-like Fibril


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The cytotoxic Staphylococcus aureus PSM alpha 3 reveals a cross-alpha amyloid-like fibril.

Tayeb-Fligelman, E.Tabachnikov, O.Moshe, A.Goldshmidt-Tran, O.Sawaya, M.R.Coquelle, N.Colletier, J.P.Landau, M.

(2017) Science 355: 831-833

  • DOI: 10.1126/science.aaf4901

  • PubMed Abstract: 
  • Amyloids are ordered protein aggregates, found in all kingdoms of life, and are involved in aggregation diseases as well as in physiological activities. In microbes, functional amyloids are often key virulence determinants, yet the structural basis f ...

    Amyloids are ordered protein aggregates, found in all kingdoms of life, and are involved in aggregation diseases as well as in physiological activities. In microbes, functional amyloids are often key virulence determinants, yet the structural basis for their activity remains elusive. We determined the fibril structure and function of the highly toxic, 22-residue phenol-soluble modulin α3 (PSMα3) peptide secreted by Staphylococcus aureus PSMα3 formed elongated fibrils that shared the morphological and tinctorial characteristics of canonical cross-β eukaryotic amyloids. However, the crystal structure of full-length PSMα3, solved de novo at 1.45 angstrom resolution, revealed a distinctive "cross-α" amyloid-like architecture, in which amphipathic α helices stacked perpendicular to the fibril axis into tight self-associating sheets. The cross-α fibrillation of PSMα3 facilitated cytotoxicity, suggesting that this assembly mode underlies function in S. aureus.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Psm alpha-3
A
22Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: psmA3
Find proteins for P0C805 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P0C805
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.143 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 29.460α = 90.00
b = 10.510β = 111.98
c = 29.710γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
Arcimboldophasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
U.S.-Israel Binational Science Foundation (BSF)United States2013254
I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation, Center of Excellence in Integrated Structural Cell BiologyIsrael1775/12
the Support for training and career development of researchers (Marie Curie) CIG, Seventh framework program (FP7) of the European Commission, Single BeneficiaryIsrael334260

Revision History 

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-03-08
    Type: Database references