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- EMDB-50515: PomX filament from Myxococcus xanthus -

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Basic information

Entry
Database: EMDB / ID: EMD-50515
TitlePomX filament from Myxococcus xanthus
Map data
Sample
  • Complex: filaments of PomX
Keywordsprokaryotes / intermediate filaments / PROTEIN FIBRIL
Biological speciesMyxococcus xanthus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 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) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50515.png

Downloads & links

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Map

FileDownload / File: emd_50515.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 200 pix.
= 436. Å		2.18 Å/pix.
x 200 pix.
= 436. Å		2.18 Å/pix.
x 200 pix.
= 436. Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.83
Minimum - Maximum-1.4294245 - 3.3007042
Average (Standard dev.)0.007262861 (±0.089402586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 436.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50515_msk_1.map
Projections & Slices
AxesZYX

Projections

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Half map: #2

Fileemd_50515_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50515_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Sample components

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Entire : filaments of PomX

EntireName: filaments of PomX
Components
  • Complex: filaments of PomX

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Supramolecule #1: filaments of PomX

SupramoleculeName: filaments of PomX / 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
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 20mM Tris/HCl; 200mM NaCl; 1mM EDTA; pH 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsTo purify PomX-His6 plasmid pEMR3 was propagated in E. coli(DE3) cells (NEB). Cells were grown in LB medium with kanamycin at 30 degree to an OD600 of 0.6. Protein accumulation was induced with 0.5mM IPTG for 16 hrs at 18 degree.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 17653 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 2150525 / Details: template free filament tracing from cryoSPARC
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC (ver. 3.4), RELION (ver. 4.0)) / Number images used: 161664
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.4)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 3.4)
FSC plot (resolution estimation)

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