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- EMDB-29800: 70S global refined map of E.coli 70S ribosome complexed with A-si... -

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Basic information

Entry
Database: EMDB / ID: EMD-29800
Title70S global refined map of E.coli 70S ribosome complexed with A-site meta-aminobenzoic acid charged tRNAPhe
Map data70S global map
Sample
  • Complex: 70S subunit of E.coli ribosome
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.31 Å
AuthorsMajumdar C / Cate JHD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 2002182 United States
CitationJournal: To Be Published
Title: 70S global refined map of E.coli 70S ribosome complexed with A-site meta-aminobenzoic acid charged tRNAPhe
Authors: Majumdar C / Cate JHD
History
DepositionFeb 16, 2023-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29800.png

Downloads & links

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Map

FileDownload / File: emd_29800.map.gz / Format: CCP4 / Size: 465.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation70S global map
Voxel sizeX=Y=Z: 0.7125 Å
Density
Contour LevelBy AUTHOR: 0.0299
Minimum - Maximum-0.111903965 - 0.26186168
Average (Standard dev.)0.00056894333 (±0.006805278)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions496496496
Spacing496496496
CellA=B=C: 353.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: 70S global refinement half map

Fileemd_29800_half_map_1.map
Annotation70S global refinement half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 70S global refinement half map

Fileemd_29800_half_map_2.map
Annotation70S global refinement half 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 : 70S subunit of E.coli ribosome

EntireName: 70S subunit of E.coli ribosome
Components
  • Complex: 70S subunit of E.coli ribosome

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Supramolecule #1: 70S subunit of E.coli ribosome

SupramoleculeName: 70S subunit of E.coli ribosome / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#34
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600

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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
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 nm
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 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:

8ebb

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 144049
FSC plot (resolution estimation)

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