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- EMDB-35905: The global structure of pre50S related to DbpA in state2 -

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Basic information

Entry
Database: EMDB / ID: EMD-35905
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: 2.92 Å
AuthorsYu T / Zeng F
Funding support China, 5 items
OrganizationGrant numberCountry
Other governmentJCYJ20220530115210023
National Natural Science Foundation of China (NSFC)32171200 China
National Natural Science Foundation of China (NSFC)92169111 China
Other government2021A1515010805
Other government2021QN02Y353
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_35905.png

Downloads & links

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Map

FileDownload / File: emd_35905.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.0119
Minimum - Maximum-0.034623314 - 0.07356372
Average (Standard dev.)0.0000037872785 (±0.0031142917)
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_35905_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_35905_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 / Material: COPPER / Mesh: 300 / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
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

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationSoftware - Name: RELION (ver. 3.1.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.0)
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60243
FSC plot (resolution estimation)

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