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- EMDB-43835: Structure of biofilm-forming functional amyloid PSMa1 from Staphy... -
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Open data
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Basic information
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Title | Structure of biofilm-forming functional amyloid PSMa1 from Staphylococcus aureus | |||||||||
![]() | DeepEM processed map. | |||||||||
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![]() | functional amyloid fibril / biofilm / bacterial biofilm / phenol soluble modulin alpha1 / PSMa1 / STRUCTURAL PROTEIN | |||||||||
Function / homology | Phenol-soluble modulin alpha peptide / Phenol-soluble modulin alpha peptide family / killing of cells of another organism / Phenol-soluble modulin alpha 1 peptide![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Hansen KH / Byeon CH / Liu Q / Drace T / Boesen T / Conway JF / Andreasen M / Akbey U | |||||||||
Funding support | 1 items
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 93.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.2 KB 23.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.9 KB | Display | ![]() |
Images | ![]() | 61 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 50.6 MB 52.4 MB 97 MB 95.5 MB 95.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 23.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9atwMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | DeepEM processed map. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.647 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: CryoSparc output unsharpened.
File | emd_43835_additional_1.map | ||||||||||||
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Annotation | CryoSparc output unsharpened. | ||||||||||||
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Density Histograms |
-Additional map: CryoSparc sharpened to B:-100
File | emd_43835_additional_2.map | ||||||||||||
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Annotation | CryoSparc sharpened to B:-100 | ||||||||||||
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Density Histograms |
-Additional map: CryoSparc auto-sharpened
File | emd_43835_additional_3.map | ||||||||||||
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Annotation | CryoSparc auto-sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map B from CryoSparc
File | emd_43835_half_map_1.map | ||||||||||||
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Annotation | Half Map B from CryoSparc | ||||||||||||
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Density Histograms |
-Half map: Half Map A from CryoSparc
File | emd_43835_half_map_2.map | ||||||||||||
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Annotation | Half Map A from CryoSparc | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1)
Entire | Name: Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1) |
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Components |
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-Supramolecule #1: Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1)
Supramolecule | Name: 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 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Phenol-soluble modulin alpha 1 peptide
Macromolecule | Name: Phenol-soluble modulin alpha 1 peptide / type: protein_or_peptide / ID: 1 / Number of copies: 64 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 2.262817 KDa |
Sequence | String: MGIIAGIIKV IKSLIEQFTG K UniProtKB: Phenol-soluble modulin alpha 1 peptide |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.8 / Details: water |
Grid | Model: 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 |
Vitrification | Cryogen 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.. |
Details | 3 microL of PSMa1 (0.5 mg/mL) was applied to grids Blotted for 6s |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen 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
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT / Overall B value: 50 |
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Output model | ![]() PDB-9atw: |