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- EMDB-44811: WT 12C IM fraction, D-b4 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-44811
TitleWT 12C IM fraction, D-b4
Map dataWT 12C IM fraction, D-b4
Sample
  • Complex: WT 12C 50S ribosomal subunit assembly intermediate
Keywords50S subunit / assembly intermediate / RNA-protein complex / ribosome
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.36 Å
AuthorsLee J / Sheng K / Williamson JR
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136412 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM053757 United States
CitationJournal: To Be Published
Title: 50S ribosome assembly intermediates at low temperature reveal bound RluB
Authors: Lee J / Sheng K / Williamson JR / Gebert L
History
DepositionMay 10, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44811.png

Downloads & links

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Map

FileDownload / File: emd_44811.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWT 12C IM fraction, D-b4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 336 pix.
= 386.4 Å		1.15 Å/pix.
x 336 pix.
= 386.4 Å		1.15 Å/pix.
x 336 pix.
= 386.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-0.31516445 - 0.9485946
Average (Standard dev.)-0.00026419674 (±0.069068246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 386.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: WT 12C IM fraction, D-b4, half map A

Fileemd_44811_half_map_1.map
AnnotationWT 12C IM fraction, D-b4, half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: WT 12C IM fraction, D-b4, half map B

Fileemd_44811_half_map_2.map
AnnotationWT 12C IM fraction, D-b4, half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : WT 12C 50S ribosomal subunit assembly intermediate

EntireName: WT 12C 50S ribosomal subunit assembly intermediate
Components
  • Complex: WT 12C 50S ribosomal subunit assembly intermediate

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Supramolecule #1: WT 12C 50S ribosomal subunit assembly intermediate

SupramoleculeName: WT 12C 50S ribosomal subunit assembly intermediate / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BW25113

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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
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris Hydrochloride
100.0 mMNH4ClAmmonium Chloride
10.0 mMMgCl2Magnesium Chloride
0.5 mMC10H16N2O8Ethylenediaminetetraacetic Acid
6.0 mMC2H6OSBeta-mercaptoethanol

Details: Most of the sucrose was removed by spin concentration.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 3 microliter of the sample was added..

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
DetailsIn order to account for highly preferred orientation of the specimen, data were acquired using tilts at -20 degrees.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 5.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Ab initio reconstruction in CryoSPARC was used.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 4217
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Non-uniform Refinement of cryoSPARC was used.
FSC plot (resolution estimation)

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