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- PDB-8qhs: Cryo-EM structure of the monocin tail-tube, MttP. -

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Basic information

Entry
Database: PDB / ID: 8qhs
TitleCryo-EM structure of the monocin tail-tube, MttP.
ComponentsAntigen A
KeywordsTOXIN / Listeria / monocytogenes / tailocins
Function / homologyPhage major tail protein TP901-1 / Phage tail tube protein / Antigen A
Function and homology information
Biological speciesListeria monocytogenes 10403S (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsNadejda, S. / Lichtenstein, R. / Schlussel, S. / Azulay, G. / Borovok, I. / Holdengraber, V. / Elad, N. / Wolf, S.G. / Zalk, R. / Zarivach, R. ...Nadejda, S. / Lichtenstein, R. / Schlussel, S. / Azulay, G. / Borovok, I. / Holdengraber, V. / Elad, N. / Wolf, S.G. / Zalk, R. / Zarivach, R. / Frank, G.A. / Herskovits, A.A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)817842European Union
CitationJournal: Nat Microbiol / Year: 2024
Title: Specialized Listeria monocytogenes produce tailocins to provide a population-level competitive growth advantage.
Authors: Nadejda Sigal / Rotem Lichtenstein-Wolfheim / Shai Schlussel / Gil Azulay / Ilya Borovok / Vered Holdengraber / Nadav Elad / Sharon G Wolf / Ran Zalk / Raz Zarivach / Gabriel A Frank / Anat A Herskovits /
Abstract: Tailocins are phage tail-like bacteriocins produced by various bacterial species to kill kin competitors. Given that tailocin release is dependent upon cell lysis, regulation of tailocin production ...Tailocins are phage tail-like bacteriocins produced by various bacterial species to kill kin competitors. Given that tailocin release is dependent upon cell lysis, regulation of tailocin production at the single-cell and population level remains unclear. Here we used flow cytometry, competition assays and structural characterization of tailocin production in a human bacterial pathogen, Listeria monocytogenes. We revealed that a specialized subpopulation, constituting less than 1% of the total bacterial population, differentiates to produce, assemble and store thousands of tailocin particles. Tailocins are packed in a highly ordered manner, clustered in a liquid crystalline phase that occupies a substantial volume of the cell. Tailocin production confers a competitive growth advantage for the rest of the population. This study provides molecular insights into tailocin production as a form of altruism, showing how cell specialization within bacterial populations can confer competitive advantages at the population level.
History
DepositionSep 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
Revision 1.2Jan 8, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antigen A
C: Antigen A
D: Antigen A
E: Antigen A
F: Antigen A


Theoretical massNumber of molelcules
Total (without water)90,0515
Polymers90,0515
Non-polymers00
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Antigen A


Mass: 18010.260 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes 10403S (bacteria)
Gene: LMRG_02367 / Production host: Listeria monocytogenes 10403S (bacteria) / References: UniProt: A0A0H3GGY8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Listeria monocytogenes 10403S monocin tail tube comprised of LMRG_02367 tail tube protein (MttP)
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 1 kDa/nm / Experimental value: NO
Source (natural)Organism: Listera (plant)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 30 % / Chamber temperature: 20 K / Details: Homemade pneumatic apparatus

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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 defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 49.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV
Image scansMovie frames/image: 50

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.1.2particle selection
2EPU2.11image acquisition
4cryoSPARC4.1.2CTF correctionlocal ctf refinement
13cryoSPARC4.1.23D reconstructionHelical Refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 25.078 ° / Axial rise/subunit: 39.297 Å / Axial symmetry: C6
Particle selectionNum. of particles selected: 503874
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 490830 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0065965
ELECTRON MICROSCOPYf_angle_d0.5818035
ELECTRON MICROSCOPYf_dihedral_angle_d5.633810
ELECTRON MICROSCOPYf_chiral_restr0.045895
ELECTRON MICROSCOPYf_plane_restr0.0031035

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