5I55

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

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

  • Deposited: 2016-02-14 Released: 2017-03-01 
  • Deposition Author(s): Landau, M., Moshe, A., Tayeb-Fligelman, E., Sawaya, M.R., Coquelle, N., Colletier, J.-P.
  • Funding Organization(s): United States - Israel Binational Science Foundation (BSF), I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation, Center of Excellence in Integrated Structural Cell Biology, the Support for training and career development of researchers (Marie Curie) CIG, Seventh framework program (FP7) of the European Commission, Single Beneficiary

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1126/science.aaf4901
  • Primary Citation of Related Structures:  
    5I55

  • 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 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   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Psm alpha-322Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for P0C805 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore P0C805 
Go to UniProtKB:  P0C805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C805
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD
Download Ideal Coordinates CCD File 
B [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT
Query on ACT
Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D 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 
  • R-Value Observed: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.46α = 90
b = 10.51β = 111.98
c = 29.71γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
Arcimboldophasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
United States - 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  (Full details and data files)

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-03-08
    Changes: Database references
  • Version 1.2: 2022-03-30
    Changes: Author supporting evidence, Database references