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- EMDB-35910: The global structure of pre50S related to DbpA in state2 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-35910
TitleThe global structure of pre50S related to DbpA in state2
Map data
Sample
  • Complex: Ribosomal 50S subunit
KeywordsRibosome / Biogenesis / pre50S / DbpA
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYu T / Zeng F
Funding support China, 5 items
OrganizationGrant numberCountry
Shenzhen Science and Technology ProgramJCYJ20220530115210023 China
National Natural Science Foundation of China (NSFC)32171200 China
National Natural Science Foundation of China (NSFC)92169111 China
Guangdong Basic and Applied Basic Research Foundation2021A1515010805 China
Major Talent Introduction Program in Guangdong Province2021QN02Y353 China
CitationJournal: To Be Published
Title: PTC Remodeling in Pre50S Intermediates: Insights into the Role of DEAD-box RNA Helicase DbpA
Authors: Yu T / Jiang J / Yu Q / Li X / Dong W / Zeng F
History
DepositionApr 11, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35910.png

Downloads & links

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Map

FileDownload / File: emd_35910.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.)
1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00546
Minimum - Maximum-0.026704757 - 0.037465885
Average (Standard dev.)0.000006415614 (±0.0018623159)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 403.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35910_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_35910_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 : Ribosomal 50S subunit

EntireName: Ribosomal 50S subunit
Components
  • Complex: Ribosomal 50S subunit

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Supramolecule #1: Ribosomal 50S subunit

SupramoleculeName: Ribosomal 50S subunit / type: complex / ID: 1 / Parent: 0 / Details: Sample was purified by polysome profiling
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
Details: 25mM HEPES-KOH,pH7.5; 140mM NH4Cl; 10mM Mg2+; 1mM DTT
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 4 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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: 2.5 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: PDB ENTRY
PDB model - PDB ID:

7k00

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26759
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.0)
FSC plot (resolution estimation)

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