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- EMDB-43835: Structure of biofilm-forming functional amyloid PSMa1 from Staphy... -

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Basic information

Entry
Database: EMDB / ID: EMD-43835
TitleStructure of biofilm-forming functional amyloid PSMa1 from Staphylococcus aureus
Map dataDeepEM processed map.
Sample
  • Complex: Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1)
    • Protein or peptide: Phenol-soluble modulin alpha 1 peptide
Keywordsfunctional amyloid fibril / biofilm / bacterial biofilm / phenol soluble modulin alpha1 / PSMa1 / STRUCTURAL PROTEIN
Function / homologyPhenol-soluble modulin alpha peptide / Phenol-soluble modulin alpha peptide family / killing of cells of another organism / Phenol-soluble modulin alpha 1 peptide
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHansen KH / Byeon CH / Liu Q / Drace T / Boesen T / Conway JF / Andreasen M / Akbey U
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structure of biofilm-forming functional amyloid PSMα1 from .
Authors: Kasper Holst Hansen / Chang Hyeock Byeon / Qian Liu / Taner Drace / Thomas Boesen / James F Conway / Maria Andreasen / Ümit Akbey /
Abstract: Biofilm-protected pathogenic causes chronic infections that are difficult to treat. An essential building block of these biofilms are functional amyloid fibrils that assemble from phenol-soluble ...Biofilm-protected pathogenic causes chronic infections that are difficult to treat. An essential building block of these biofilms are functional amyloid fibrils that assemble from phenol-soluble modulins (PSMs). PSMα1 cross-seeds other PSMs into cross-β amyloid folds and is therefore a key element in initiating biofilm formation. However, the paucity of high-resolution structures hinders efforts to prevent amyloid assembly and biofilm formation. Here, we present a 3.5 Å resolution density map of the major PSMα1 fibril form revealing a left-handed cross-β fibril composed of two C-symmetric U-shaped protofilaments whose subunits are unusually tilted out-of-plane. Monomeric α-helical PSMα1 is extremely cytotoxic to cells, despite the moderate toxicity of the cross-β fibril. We suggest mechanistic insights into the PSM functional amyloid formation and conformation transformation on the path from monomer-to-fibril formation. Details of PSMα1 assembly and fibril polymorphism suggest how utilizes functional amyloids to form biofilms and establish a framework for developing therapeutics against infection and antimicrobial resistance.
History
DepositionFeb 27, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43835.png

Downloads & links

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Map

FileDownload / File: emd_43835.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEM processed map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 300 pix.
= 194.1 Å		0.65 Å/pix.
x 300 pix.
= 194.1 Å		0.65 Å/pix.
x 300 pix.
= 194.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.000914374 - 1.7745667
Average (Standard dev.)0.0134513 (±0.08805764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 194.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43835_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoSparc output unsharpened.

Fileemd_43835_additional_1.map
AnnotationCryoSparc output unsharpened.
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoSparc sharpened to B:-100

Fileemd_43835_additional_2.map
AnnotationCryoSparc sharpened to B:-100
Projections & Slices
AxesZYX

Projections

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Histogram

Histogram (log scale)

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Additional map: CryoSparc auto-sharpened

Fileemd_43835_additional_3.map
AnnotationCryoSparc auto-sharpened
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B from CryoSparc

Fileemd_43835_half_map_1.map
AnnotationHalf Map B from CryoSparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A from CryoSparc

Fileemd_43835_half_map_2.map
AnnotationHalf Map A from CryoSparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1)

EntireName: Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1)
Components
  • Complex: Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1)
    • Protein or peptide: Phenol-soluble modulin alpha 1 peptide

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Supramolecule #1: Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1)

SupramoleculeName: Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Biofilm forming functional amyloid from Staphylococcus aureus PSMa1 is produced by peptide-synthesis
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: Phenol-soluble modulin alpha 1 peptide

MacromoleculeName: Phenol-soluble modulin alpha 1 peptide / type: protein_or_peptide / ID: 1 / Number of copies: 64 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 2.262817 KDa
SequenceString:
MGIIAGIIKV IKSLIEQFTG K

UniProtKB: Phenol-soluble modulin alpha 1 peptide

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.8 / Details: water
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
Details: C-Flat R2/2 Cu 300 mesh holey carbon grids (Protochips) were glow discharged for 45 s at 15 mA using a Quorum GloQube Plus
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 99 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: plunge-frozen in liquid ethane using a Vitrobot Mark IV plunge freezer with a blot force of zero at 4C and 99% humidity..
Details3 microL of PSMa1 (0.5 mg/mL) was applied to grids Blotted for 6s

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3002 / Average exposure time: 1.5 sec. / Average electron dose: 63.0 e/Å2
Details: A total of 3,002 movies of the PSMa1 sample were collected
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.95 Å
Applied symmetry - Helical parameters - Δ&Phi: -3.578 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1)
Details: The overall resolution estimated by CryoSPARC was 3.51A according to the gold standard Fourier shell correlation cutoff at 0.143. The final map was sharpened by using DeepEMhancer
Number images used: 100
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT / Overall B value: 50
Output model

PDB-9atw:
Structure of biofilm-forming functional amyloid PSMa1 from Staphylococcus aureus

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