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- EMDB-50504: in situ 70S Myxococcus xanthus ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-50504
Titlein situ 70S Myxococcus xanthus ribosome
Map data
Sample
  • Complex: in situ subtomo averaging of Myxococcus xanthus ribosome
Keywordsin situ Subtomogram averaging / Myxococcus xanthus / RIBOSOME
Biological speciesMyxococcus xanthus (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 6.0 Å
AuthorsXu P / Schumacher D / Liu C / Dickmanns M / Beck F / Plitzko J / Baumeister W / Sogaard-Andersen L
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: In situ architecture of a nucleoid-associated biomolecular co-condensate that regulates bacterial cell division.
Authors: Peng Xu / Dominik Schumacher / Chuan Liu / Andrea Harms / Marcel Dickmanns / Florian Beck / Jürgen M Plitzko / Wolfgang Baumeister / Lotte Søgaard-Andersen /
Abstract: In most bacteria, cell division depends on the tubulin-homolog FtsZ that polymerizes in a GTP-dependent manner to form the cytokinetic Z-ring at the future division site. Subsequently, the Z-ring ...In most bacteria, cell division depends on the tubulin-homolog FtsZ that polymerizes in a GTP-dependent manner to form the cytokinetic Z-ring at the future division site. Subsequently, the Z-ring recruits, directly or indirectly, all other proteins of the divisome complex that executes cytokinesis. A critical step in this process is the precise positioning of the Z-ring at the future division site. While the divisome proteins are generally conserved, the regulatory systems that position the Z-ring are more diverse. However, these systems have in common that they modulate FtsZ polymerization. In PomX, PomY, and PomZ form precisely one MDa-sized, nonstoichiometric, nucleoid-associated assembly that spatiotemporally guides Z-ring formation. Here, using cryo-correlative light and electron microscopy together with in situ cryoelectron tomography, we determine the PomXYZ assembly's architecture at close-to-live conditions. PomX forms a porous meshwork of randomly intertwined filaments. Templated by this meshwork, the phase-separating PomY protein forms a biomolecular condensate that compacts and bends the PomX filaments, resulting in the formation of a selective PomXYZ co-condensate that is associated to the nucleoid by PomZ. These studies reveal a hitherto undescribed supramolecular structure and provide a framework for understanding how a nonstoichiometric co-condensate forms, maintains number control, and nucleates GTP-dependent FtsZ polymerization to precisely regulate cell division.
History
DepositionMay 31, 2024-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50504.png

Downloads & links

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Map

FileDownload / File: emd_50504.map.gz / Format: CCP4 / Size: 78.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
2.93 Å/pix.
x 274 pix.
= 802.82 Å		2.93 Å/pix.
x 274 pix.
= 802.82 Å		2.93 Å/pix.
x 274 pix.
= 802.82 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.93 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0135
Minimum - Maximum-0.014679201 - 0.049643494
Average (Standard dev.)0.000024270417 (±0.0023033272)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions274274274
Spacing274274274
CellA=B=C: 802.82 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50504_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50504_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : in situ subtomo averaging of Myxococcus xanthus ribosome

EntireName: in situ subtomo averaging of Myxococcus xanthus ribosome
Components
  • Complex: in situ subtomo averaging of Myxococcus xanthus ribosome

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Supramolecule #1: in situ subtomo averaging of Myxococcus xanthus ribosome

SupramoleculeName: in situ subtomo averaging of Myxococcus xanthus ribosome
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Myxococcus xanthus (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsM. xanthus was grown in 1% CTT broth (1% (w/v) Bacto Casitone, 10mM Tris-HCl pH 8.0, 1mM K2HPO4/KH2PO4 pH 7.6, 8mM MgSO4) to OD600~=1.8

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 42000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. 1.0.9) / Software - details: Warp/M uses RELION alignments as inputs / Number subtomograms used: 8087
ExtractionNumber tomograms: 24 / Number images used: 14212 / Reference model: EMD-3493 / Method: template match / Software - Name: STOPGAP (ver. 0.7.3) / Details: lowpass reference model to 40A for template match
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0) / Details: remove bad particles
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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