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- EMDB-38958: 45S State C under 1 mM magnesium when overexpressing DbpA-R331A -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-38958
Title45S State C under 1 mM magnesium when overexpressing DbpA-R331A
Map data
Sample
  • Complex: 45S state C under 1 mM magnesium when overexpressing wild type DbpA
Keywordspre50S / ribosome / DbpA
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsYu T / Zeng F
Funding support China, 1 items
OrganizationGrant numberCountry
Other governmentJCYJ20220530115210023 China
CitationJournal: To Be Published
Title: PTC remodeling in pre50S intermediates: insights into the role of DEAD-box RNA helicase DbpA
Authors: Yu T / Yu Q / Jiang J / Li X / Huang Z / Zeng F
History
DepositionFeb 1, 2024-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38958.png

Downloads & links

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Map

FileDownload / File: emd_38958.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.035229623 - 0.06347543
Average (Standard dev.)0.000032920718 (±0.0017561166)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 414.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38958_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38958_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 45S state C under 1 mM magnesium when overexpressing wild type DbpA

EntireName: 45S state C under 1 mM magnesium when overexpressing wild type DbpA
Components
  • Complex: 45S state C under 1 mM magnesium when overexpressing wild type DbpA

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Supramolecule #1: 45S state C under 1 mM magnesium when overexpressing wild type DbpA

SupramoleculeName: 45S state C under 1 mM magnesium when overexpressing wild type DbpA
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

22586

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 165548
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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