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- PDB-9atw: Structure of biofilm-forming functional amyloid PSMa1 from Staphy... -

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Basic information

Entry
Database: PDB / ID: 9atw
TitleStructure of biofilm-forming functional amyloid PSMa1 from Staphylococcus aureus
ComponentsPhenol-soluble modulin alpha 1 peptide
KeywordsSTRUCTURAL PROTEIN / functional amyloid fibril / biofilm / bacterial biofilm / phenol soluble modulin alpha1 / PSMa1
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHansen, K.H. / Byeon, C.H. / Liu, Q. / Drace, T. / Boesen, T. / Conway, J.F. / Andreasen, M. / Akbey, U.
Funding support1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Data collection / Derived calculations
Category: em_admin / struct_sheet ...em_admin / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _em_admin.last_update
Revision 1.2Aug 21, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AU: Phenol-soluble modulin alpha 1 peptide
AV: Phenol-soluble modulin alpha 1 peptide
AW: Phenol-soluble modulin alpha 1 peptide
AX: Phenol-soluble modulin alpha 1 peptide
AY: Phenol-soluble modulin alpha 1 peptide
AZ: Phenol-soluble modulin alpha 1 peptide
Aa: Phenol-soluble modulin alpha 1 peptide
Ab: Phenol-soluble modulin alpha 1 peptide
Ac: Phenol-soluble modulin alpha 1 peptide
Ad: Phenol-soluble modulin alpha 1 peptide
Ae: Phenol-soluble modulin alpha 1 peptide
Af: Phenol-soluble modulin alpha 1 peptide
Ag: Phenol-soluble modulin alpha 1 peptide
Ah: Phenol-soluble modulin alpha 1 peptide
Ai: Phenol-soluble modulin alpha 1 peptide
Aj: Phenol-soluble modulin alpha 1 peptide
Ak: Phenol-soluble modulin alpha 1 peptide
Al: Phenol-soluble modulin alpha 1 peptide
Am: Phenol-soluble modulin alpha 1 peptide
An: Phenol-soluble modulin alpha 1 peptide
Ao: Phenol-soluble modulin alpha 1 peptide
Ap: Phenol-soluble modulin alpha 1 peptide
Aq: Phenol-soluble modulin alpha 1 peptide
Ar: Phenol-soluble modulin alpha 1 peptide
As: Phenol-soluble modulin alpha 1 peptide
At: Phenol-soluble modulin alpha 1 peptide
Au: Phenol-soluble modulin alpha 1 peptide
Av: Phenol-soluble modulin alpha 1 peptide
Aw: Phenol-soluble modulin alpha 1 peptide
Ax: Phenol-soluble modulin alpha 1 peptide
Ay: Phenol-soluble modulin alpha 1 peptide
Az: Phenol-soluble modulin alpha 1 peptide
A1: Phenol-soluble modulin alpha 1 peptide
A2: Phenol-soluble modulin alpha 1 peptide
A3: Phenol-soluble modulin alpha 1 peptide
A4: Phenol-soluble modulin alpha 1 peptide
A5: Phenol-soluble modulin alpha 1 peptide
A6: Phenol-soluble modulin alpha 1 peptide
A7: Phenol-soluble modulin alpha 1 peptide
A8: Phenol-soluble modulin alpha 1 peptide
A9: Phenol-soluble modulin alpha 1 peptide
A0: Phenol-soluble modulin alpha 1 peptide
BA: Phenol-soluble modulin alpha 1 peptide
BB: Phenol-soluble modulin alpha 1 peptide
BC: Phenol-soluble modulin alpha 1 peptide
BD: Phenol-soluble modulin alpha 1 peptide
BE: Phenol-soluble modulin alpha 1 peptide
BF: Phenol-soluble modulin alpha 1 peptide
BG: Phenol-soluble modulin alpha 1 peptide
BH: Phenol-soluble modulin alpha 1 peptide
BI: Phenol-soluble modulin alpha 1 peptide
BJ: Phenol-soluble modulin alpha 1 peptide
BK: Phenol-soluble modulin alpha 1 peptide
BL: Phenol-soluble modulin alpha 1 peptide
BM: Phenol-soluble modulin alpha 1 peptide
BN: Phenol-soluble modulin alpha 1 peptide
BO: Phenol-soluble modulin alpha 1 peptide
BP: Phenol-soluble modulin alpha 1 peptide
BQ: Phenol-soluble modulin alpha 1 peptide
BR: Phenol-soluble modulin alpha 1 peptide
BS: Phenol-soluble modulin alpha 1 peptide
BT: Phenol-soluble modulin alpha 1 peptide
BU: Phenol-soluble modulin alpha 1 peptide
BV: Phenol-soluble modulin alpha 1 peptide


Theoretical massNumber of molelcules
Total (without water)144,82064
Polymers144,82064
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide ...
Phenol-soluble modulin alpha 1 peptide


Mass: 2262.817 Da / Num. of mol.: 64 / Fragment: UNP residues 1-21 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria) / References: UniProt: A9JX05

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: 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
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Buffer solutionpH: 7.8 / Details: water
SpecimenConc.: 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 supportDetails: 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
VitrificationInstrument: 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2EPUv2.7image acquisition
4cryoSPARC4.1CTF correction
7UCSF ChimeraX1.8model fitting
9cryoSPARC4.1initial Euler assignment
10cryoSPARC4.1final Euler assignment
11cryoSPARC4.1classification
12cryoSPARC4.13D reconstruction
13PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -3.578 ° / Axial rise/subunit: 4.95 Å / Axial symmetry: C2
3D reconstructionResolution: 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 buildingB value: 50 / Protocol: FLEXIBLE FIT

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