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- PDB-7t8u: Structure of PSMbeta2 nanotubes -

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Basic information

Entry
Database: PDB / ID: 7t8u
TitleStructure of PSMbeta2 nanotubes
ComponentsAntibacterial proteinAntibiotic
KeywordsPROTEIN FIBRIL / nanotubes / amyloid / cross-alpha
Function / homologyPhenol-soluble modulin beta protein / Phenol-soluble modulin beta protein / Antibacterial protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKreutzberger, M.A. / Wang, S. / Egelman, E.H. / Conicello, V.P.
Funding support United States, 2items
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
DepositionDec 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibacterial protein
B: Antibacterial protein
C: Antibacterial protein
D: Antibacterial protein


Theoretical massNumber of molelcules
Total (without water)17,8364
Polymers17,8364
Non-polymers00
Water0
1
A: Antibacterial protein
B: Antibacterial protein
C: Antibacterial protein
D: Antibacterial protein
x 120


Theoretical massNumber of molelcules
Total (without water)2,140,371480
Polymers2,140,371480
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
helical symmetry operation119
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 6 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 120 / Rise per n subunits: 8.3 Å / Rotation per n subunits: 28.6 °)

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Components

#1: Protein/peptide
Antibacterial protein / Antibiotic / Antibacterial protein 3 / Antibacterial protein 3 homolog / Psm beta2 / Uncharacterized protein


Mass: 4459.106 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria) / References: UniProt: H9BRQ4

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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: PSMbeta2 nanotubes / Type: COMPLEX / Entity ID: all / Source: SYNTHETIC
Source (natural)Organism: Staphylococcus aureus (bacteria)
Buffer solutionpH: 10 / Details: 10 mM CAPS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2250 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 28.6 ° / Axial rise/subunit: 8.3 Å / Axial symmetry: C6
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44441 / Symmetry type: HELICAL

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