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- EMDB-47539: Representative tomogram of WT-PopZ condensate -

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Basic information

Entry
Database: EMDB / ID: EMD-47539
TitleRepresentative tomogram of WT-PopZ condensate
Map datatomogram
Sample
  • Complex: polar organizing protein Z (PopZ)
KeywordsCondensate / phase separation / bacteria / PROTEIN FIBRIL
Biological speciesCaulobacter vibrioides (bacteria)
Methodelectron tomography / cryo EM
AuthorsLasker K / Park D
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: The filamentous ultrastructure of the PopZ condensate is required for its cellular function.
Authors: Daniel Scholl / Tumara Boyd / Andrew P Latham / Alexandra Salazar / Asma M A M Khan / Steven Boeynaems / Alex S Holehouse / Gabriel C Lander / Andrej Sali / Donghyun Park / Ashok A Deniz / Keren Lasker /
Abstract: Biomolecular condensates have key roles in regulating cellular processes. Yet, the relationship between atomic features and condensate function remains poorly understood. We studied this relationship ...Biomolecular condensates have key roles in regulating cellular processes. Yet, the relationship between atomic features and condensate function remains poorly understood. We studied this relationship using the polar organizing protein Z (PopZ). Here, we revealed hierarchical assembly of PopZ into a filamentous condensate by integrating cryo-electron tomography, biochemistry, single-molecule techniques and molecular dynamics simulations. The PopZ helical domain drives filamentation and condensation, while the disordered region inhibits them. Phase-dependent conformational changes prevent interfilament contacts in the dilute phase and expose client-binding sites in the dense phase. Perturbing filament formation in vitro alters the dynamics of scaffold and client proteins and the condensate's wetting behavior. In cells, perturbing either filament formation or the ability of filaments to condense impairs PopZ function and leads to growth phenotypes. These findings establish a multiscale framework linking molecular interactions and condensate ultrastructure to cellular function.
History
DepositionOct 28, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47539.png

Downloads & links

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Map

FileDownload / File: emd_47539.map.gz / Format: CCP4 / Size: 183.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationtomogram
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.3 Å/pix.
x 131 pix.
= 1742.824 Å		13.3 Å/pix.
x 720 pix.
= 9578.88 Å		13.3 Å/pix.
x 511 pix.
= 6798.344 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: 13.304 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-37.962207999999997 - 13.043958999999999
Average (Standard dev.)-0.36883032 (±0.43509373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720511131
Spacing511720131
CellA: 6798.3438 Å / B: 9578.88 Å / C: 1742.824 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : polar organizing protein Z (PopZ)

EntireName: polar organizing protein Z (PopZ)
Components
  • Complex: polar organizing protein Z (PopZ)

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Supramolecule #1: polar organizing protein Z (PopZ)

SupramoleculeName: polar organizing protein Z (PopZ) / type: complex / ID: 1 / Parent: 0 / Details: WT sequence
Source (natural)Organism: Caulobacter vibrioides (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 35
CTF correctionType: NONE

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