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- EMDB-36860: Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-36860
TitleCryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex (Body 1)
Map data
Sample
  • Complex: Ribosome Body
KeywordsRibosome / AP-mRNA
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsRamachandran R / Afsar M / Shukla A
Funding support India, 3 items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)GAP0292 India
Council of Scientific & Industrial Research (CSIR)CII7032 & MLP0107 India
Department of Biotechnology (DBT, India)GAP0384 India
CitationJournal: To Be Published
Title: Cryo-EM structure of 30S ribosome with cleaved AP-mRNA bound complex (Body 1)
Authors: Ramachandran R / Afsar M / Shukla A
History
DepositionJul 17, 2023-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36860.png

Downloads & links

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Map

FileDownload / File: emd_36860.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 256 pix.
= 353.28 Å		1.38 Å/pix.
x 256 pix.
= 353.28 Å		1.38 Å/pix.
x 256 pix.
= 353.28 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0058
Minimum - Maximum-0.025430985 - 0.12290496
Average (Standard dev.)-0.00017647808 (±0.0064722933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36860_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_36860_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36860_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Ribosome Body

EntireName: Ribosome Body
Components
  • Complex: Ribosome Body

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Supramolecule #1: Ribosome Body

SupramoleculeName: Ribosome Body / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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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
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 54.0 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: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77582
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER

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