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- PDB-9atw: Structure of biofilm-forming functional amyloid PSMa1 from Staphy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9atw | ||||||
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Title | Structure of biofilm-forming functional amyloid PSMa1 from Staphylococcus aureus | ||||||
![]() | Phenol-soluble modulin alpha 1 peptide | ||||||
![]() | STRUCTURAL PROTEIN / functional amyloid fibril / biofilm / bacterial biofilm / phenol soluble modulin alpha1 / PSMa1 | ||||||
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 | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
![]() | Hansen, K.H. / Byeon, C.H. / Liu, Q. / Drace, T. / Boesen, T. / Conway, J.F. / Andreasen, M. / Akbey, U. | ||||||
Funding support | 1items
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![]() | ![]() Year: 2024 Title: Structure of biofilm-forming functional amyloid PSMa1 from Staphylococcus aureus Authors: Hansen, K.H. / Byeon, C.H. / Liu, Q. / Drace, T. / Boesen, T. / Conway, J.F. / Andreasen, M. / Akbey, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 432.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 37.6 KB | Display | |
Data in CIF | ![]() | 61.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 43835MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein/peptide | Mass: 2262.817 Da / Num. of mol.: 64 / Fragment: UNP residues 1-21 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: Phenol Soluble Modulin alpha1 (PSMAlpha1) (PSMa1) / Type: COMPLEX Details: Biofilm forming functional amyloid from Staphylococcus aureus PSMa1 is produced by peptide-synthesis Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.8 / Details: water |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: 3 microL of PSMa1 (0.5 mg/mL) was applied to grids Blotted for 6s |
Specimen support | 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 Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 99 % / Chamber temperature: 277 K Details: plunge-frozen in liquid ethane using a Vitrobot Mark IV plunge freezer with a blot force of zero at 4C and 99% humidity. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 63 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3002 Details: A total of 3,002 movies of the PSMa1 sample were collected |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -3.578 ° / Axial rise/subunit: 4.95 Å / Axial symmetry: C2 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100 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 Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 50 / Protocol: FLEXIBLE FIT |