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- EMDB-42155: Representative tomogram of PolyP + 15kb DNA -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-42155
TitleRepresentative tomogram of PolyP + 15kb DNA
Map dataPolyP 15kb
Sample
  • Organelle or cellular component: Polyphosphate
KeywordsBacteria / Condensate / Inorganic polymer / Starvation / UNKNOWN FUNCTION
Biological speciessynthetic construct (others)
Methodelectron tomography / cryo EM
AuthorsRacki LR / Deniz AA / Park D
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM130375 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2-GM-739-140918 United States
CitationJournal: Nat Commun / Year: 2024
Title: Reentrant DNA shells tune polyphosphate condensate size.
Authors: Ravi Chawla / Jenna K A Tom / Tumara Boyd / Nicholas H Tu / Tanxi Bai / Danielle A Grotjahn / Donghyun Park / Ashok A Deniz / Lisa R Racki /
Abstract: The inorganic biopolymer polyphosphate (polyP) occurs in all domains of life and affects myriad cellular processes. A longstanding observation is polyP's frequent proximity to chromatin, and, in many ...The inorganic biopolymer polyphosphate (polyP) occurs in all domains of life and affects myriad cellular processes. A longstanding observation is polyP's frequent proximity to chromatin, and, in many bacteria, its occurrence as magnesium (Mg)-enriched condensates embedded in the nucleoid region, particularly in response to stress. The physical basis of the interaction between polyP, DNA and Mg, and the resulting effects on the organization of the nucleoid and polyP condensates, remain poorly understood. Here, using a minimal system of polyP, Mg, and DNA, we find that DNA can form shells around polyP-Mg condensates. These shells show reentrant behavior, that is, they form within a window of Mg concentrations, representing a tunable architecture with potential relevance in other multicomponent condensates. This surface association tunes condensate size and DNA morphology in a manner dependent on DNA length and concentration, even at DNA concentrations orders of magnitude lower than found in the cell. Our work also highlights the remarkable capacity of two primordial inorganic species to organize DNA.
History
DepositionSep 30, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42155.png

Downloads & links

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Map

FileDownload / File: emd_42155.map.gz / Format: CCP4 / Size: 182.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPolyP 15kb
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.3 Å/pix.
x 130 pix.
= 1729. Å		13.3 Å/pix.
x 720 pix.
= 9576. Å		13.3 Å/pix.
x 511 pix.
= 6796.3 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: 13.3 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-26.306004000000001 - 10.919760999999999
Average (Standard dev.)-0.48509118 (±0.34646314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720511130
Spacing511720130
CellA: 6796.3003 Å / B: 9576.0 Å / C: 1729.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Polyphosphate

EntireName: Polyphosphate
Components
  • Organelle or cellular component: Polyphosphate

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Supramolecule #1: Polyphosphate

SupramoleculeName: Polyphosphate / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: synthetic construct (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN 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: OTHER / Nominal defocus max: 7.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 35

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