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- EMDB-12580: Cryo electron tomogram of Shigella flexneri drfaC mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-12580
TitleCryo electron tomogram of Shigella flexneri drfaC mutant
Map data
Sample
  • Cell: Shigella flexneri drfaC mutant
Biological speciesShigella flexneri (bacteria)
Methodelectron tomography / cryo EM
AuthorsLobato-Marquez D / Xu J / Ojiakor A / Pilhofer M / Mostowy S
Funding supportEuropean Union, Switzerland, 5 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionH2020-MSCA-IF-2016-752022European Union
European Research Council (ERC)772853-ENTRAPMENTEuropean Union
Wellcome Trust206444/Z/17/ZEuropean Union
European Research Council (ERC)679209European Union
Swiss National Science Foundation31003A_179255 Switzerland
CitationJournal: Nat Commun / Year: 2021
Title: Mechanistic insight into bacterial entrapment by septin cage reconstitution.
Authors: Damián Lobato-Márquez / Jingwei Xu / Gizem Özbaykal Güler / Adaobi Ojiakor / Martin Pilhofer / Serge Mostowy /
Abstract: Septins are cytoskeletal proteins that assemble into hetero-oligomeric complexes and sense micron-scale membrane curvature. During infection with Shigella flexneri, an invasive enteropathogen, ...Septins are cytoskeletal proteins that assemble into hetero-oligomeric complexes and sense micron-scale membrane curvature. During infection with Shigella flexneri, an invasive enteropathogen, septins restrict actin tail formation by entrapping bacteria in cage-like structures. Here, we reconstitute septin cages in vitro using purified recombinant septin complexes (SEPT2-SEPT6-SEPT7), and study how these recognize bacterial cells and assemble on their surface. We show that septin complexes recognize the pole of growing Shigella cells. An amphipathic helix domain in human SEPT6 enables septins to sense positively curved membranes and entrap bacterial cells. Shigella strains lacking lipopolysaccharide components are more efficiently entrapped in septin cages. Finally, cryo-electron tomography of in vitro cages reveals how septins assemble as filaments on the bacterial cell surface.
History
DepositionMar 8, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateJan 26, 2022-
Current statusJan 26, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Movie viewer
Supplemental images

emd_12580.png

Downloads & links

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Map

FileDownload / File: emd_12580.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.74 Å/pix.
x 500 pix.
= 5370. Å		10.74 Å/pix.
x 1440 pix.
= 15465.6 Å		10.74 Å/pix.
x 1024 pix.
= 10997.76 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.74 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-526.6144 - 648.06006
Average (Standard dev.)-3.1281093e-09 (±44.029892)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions14401024500
Spacing10241440500
CellA: 10997.76 Å / B: 15465.6 Å / C: 5370.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.7410.7410.74
M x/y/z10241440500
origin x/y/z0.0000.0000.000
length x/y/z10997.76015465.6005370.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS10241440500
D min/max/mean-526.614648.060-0.000

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Supplemental data

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Sample components

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Entire : Shigella flexneri drfaC mutant

EntireName: Shigella flexneri drfaC mutant
Components
  • Cell: Shigella flexneri drfaC mutant

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Supramolecule #1: Shigella flexneri drfaC mutant

SupramoleculeName: Shigella flexneri drfaC mutant / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Shigella flexneri (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE-PROPANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: cytodiagnostics / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 2.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 61

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