5I55

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

• PDB DOI: https://doi.org/10.2210/pdb5I55/pdb

• 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

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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 

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

• PubMed: 28232575 
• 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 .

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 20-mer - A20 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2.84 kDa 
• Atom Count: 218 
• Modelled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Psm alpha-3	A	22	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for P0C805 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P0C805  Go to UniProtKB:  P0C805

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	B [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 29.46	α = 90
b = 10.51	β = 111.98
c = 29.71	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
Arcimboldo	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-01 
Deposition Author(s): Landau, M., Moshe, A., Tayeb-Fligelman, E., Sawaya, M.R., Coquelle, N., Colletier, J.-P.

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Funding Organization	Location	Grant Number
United States - Israel Binational Science Foundation (BSF)	United States	2013254
I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation, Center of Excellence in Integrated Structural Cell Biology	Israel	1775/12
the Support for training and career development of researchers (Marie Curie) CIG, Seventh framework program (FP7) of the European Commission, Single Beneficiary	Israel	334260

Revision History  

• 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
• Version 1.3: 2024-10-09
  Changes: Data collection, Structure summary