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- EMDB-25584: Structure of the larger diameter PSMalpha3 nanotube -

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Basic information

Entry
Database: EMDB / ID: EMD-25584
TitleStructure of the larger diameter PSMalpha3 nanotube
Map data
Sample
  • Complex: Nanotube assembly of PSMalpha3
    • Protein or peptide: Phenol-soluble modulin PSM-alpha-3
Keywordsnanotubes / amyloid / cross-alpha / PROTEIN FIBRIL
Function / homologyPhenol-soluble modulin alpha peptide / Phenol-soluble modulin alpha peptide family / killing of cells of another organism / Phenol-soluble modulin PSM-alpha-3
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsKreutzberger MA / Wang S
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1534317 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Phenol-soluble modulins PSMα3 and PSMβ2 form nanotubes that are cross-α amyloids.
Authors: Mark A B Kreutzberger / Shengyuan Wang / Leticia C Beltran / Abraham Tuachi / Xiaobing Zuo / Edward H Egelman / Vincent P Conticello /
Abstract: Phenol-soluble modulins (PSMs) are peptide-based virulence factors that play significant roles in the pathogenesis of staphylococcal strains in community-associated and hospital-associated infections. ...Phenol-soluble modulins (PSMs) are peptide-based virulence factors that play significant roles in the pathogenesis of staphylococcal strains in community-associated and hospital-associated infections. In addition to cytotoxicity, PSMs display the propensity to self-assemble into fibrillar species, which may be mediated through the formation of amphipathic conformations. Here, we analyze the self-assembly behavior of two PSMs, PSMα3 and PSMβ2, which are derived from peptides expressed by methicillin-resistant Staphylococcus aureus (MRSA), a significant human pathogen. In both cases, we observed the formation of a mixture of self-assembled species including twisted filaments, helical ribbons, and nanotubes, which can reversibly interconvert in vitro. Cryo–electron microscopy structural analysis of three PSM nanotubes, two derived from PSMα3 and one from PSMβ2, revealed that the assemblies displayed remarkably similar structures based on lateral association of cross-α amyloid protofilaments. The amphipathic helical conformations of PSMα3 and PSMβ2 enforced a bilayer arrangement within the protofilaments that defined the structures of the respective PSMα3 and PSMβ2 nanotubes. We demonstrate that, similar to amyloids based on cross-β protofilaments, cross-α amyloids derived from these PSMs display polymorphism, not only in terms of the global morphology (e.g., twisted filament, helical ribbon, and nanotube) but also with respect to the number of protofilaments within a given peptide assembly. These results suggest that the folding landscape of PSM derivatives may be more complex than originally anticipated and that the assemblies are able to sample a wide range of supramolecular structural space.
History
DepositionNov 30, 2021-
Header (metadata) releaseMay 18, 2022-
Map releaseMay 18, 2022-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25584.png

Downloads & links

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Map

FileDownload / File: emd_25584.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.014202658 - 0.029274873
Average (Standard dev.)0.0003935274 (±0.0022351183)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Nanotube assembly of PSMalpha3

EntireName: Nanotube assembly of PSMalpha3
Components
  • Complex: Nanotube assembly of PSMalpha3
    • Protein or peptide: Phenol-soluble modulin PSM-alpha-3

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Supramolecule #1: Nanotube assembly of PSMalpha3

SupramoleculeName: Nanotube assembly of PSMalpha3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus aureus (bacteria) / Synthetically produced: Yes

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Macromolecule #1: Phenol-soluble modulin PSM-alpha-3

MacromoleculeName: Phenol-soluble modulin PSM-alpha-3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 2.611149 KDa
SequenceString:
MEFVAKLFKF FKDLLGKFLG NN

UniProtKB: Phenol-soluble modulin PSM-alpha-3

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5i55

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.13 Å
Applied symmetry - Helical parameters - Δ&Phi: -26.83 °
Applied symmetry - Helical parameters - Axial symmetry: C7 (7 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 27093

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