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- EMDB-47844: Montaged cryo-ET map of individual particle 3D reconstructions of... -

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Basic information

Entry
Database: EMDB / ID: EMD-47844
TitleMontaged cryo-ET map of individual particle 3D reconstructions of ~2 kb negatively supercoiled plasmids (delta Lk centered on -15) under near physiological salt condition (40 mM K+, 5 mM Mg2+)
Map dataMontaged cryo-ET map of individual particle 3D reconstructions of ~2 kb negatively supercoiled plasmids (delta Lk centered on -15) under near physiological salt condition (40 mM K , 5 mM Mg2 )
Sample
  • Complex: 2 kb negatively supercoiled pUC19 plasmids containing a T7A1-U promoter
KeywordsDNA Supercoiling / Transcription regulation / Cryo-Electron Tomography (cryo-ET) / Topological Domains / DNA
Biological speciesEscherichia coli (E. coli)
Methodelectron tomography / cryo EM
AuthorsZhang M / Bustamante C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Interplay Between DNA Supercoiling and RNA Polymerase Localization at Plectoneme Apices Modulate Transcription Dynamics
Authors: Zhang M / Bustamante C
History
DepositionNov 11, 2024-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47844.png

Downloads & links

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Map

FileDownload / File: emd_47844.map.gz / Format: CCP4 / Size: 915.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMontaged cryo-ET map of individual particle 3D reconstructions of ~2 kb negatively supercoiled plasmids (delta Lk centered on -15) under near physiological salt condition (40 mM K , 5 mM Mg2 )
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.69 Å/pix.
x 200 pix.
= 2338. Å		11.69 Å/pix.
x 1000 pix.
= 11690. Å		11.69 Å/pix.
x 1200 pix.
= 14027.999 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: 11.69 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.5162568 - 4.5810475
Average (Standard dev.)0.0009016721 (±0.031435337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10001200200
Spacing12001000200
CellA: 14027.999 Å / B: 11690.0 Å / C: 2338.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : 2 kb negatively supercoiled pUC19 plasmids containing a T7A1-U pr...

EntireName: 2 kb negatively supercoiled pUC19 plasmids containing a T7A1-U promoter
Components
  • Complex: 2 kb negatively supercoiled pUC19 plasmids containing a T7A1-U promoter

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Supramolecule #1: 2 kb negatively supercoiled pUC19 plasmids containing a T7A1-U pr...

SupramoleculeName: 2 kb negatively supercoiled pUC19 plasmids containing a T7A1-U promoter
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli) / Details: pUC19 plasmid

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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 / Chamber humidity: 95 % / Chamber temperature: 288 K / Instrument: LEICA EM GP
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 130.0 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: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 53000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware: (Name: EMAN2, SPIDER) / Number images used: 35
CTF correctionSoftware - Name: EMAN2 / Type: PHASE FLIPPING ONLY

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