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- EMDB-51599: 30S-TEC (TEC in expressome position) Inactive state 1, focused pl... -

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Basic information

Entry
Database: EMDB / ID: EMD-51599
Title30S-TEC (TEC in expressome position) Inactive state 1, focused platform map
Map data
Sample
  • Complex: 30S ribosomal subunit
KeywordsTranscription / translation / coupling. / RIBOSOME
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsRahil H / Weixlbaumer A / Webster MW
Funding supportEuropean Union, France, United States, United Kingdom, 6 items
OrganizationGrant numberCountry
European Research Council (ERC)679734European Union
Agence Nationale de la Recherche (ANR)ANR-10-LABX-0030-INRT France
Agence Nationale de la Recherche (ANR)ANR-10-IDEX-0002-02 France
European Molecular Biology Organization (EMBO)European Union
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131922 United States
Wellcome Trust203149 United Kingdom
CitationJournal: Science / Year: 2024
Title: Molecular basis of mRNA delivery to the bacterial ribosome.
Authors: Michael W Webster / Adrien Chauvier / Huma Rahil / Andrea Graziadei / Kristine Charles / Nataliya Miropolskaya / Maria Takacs / Charlotte Saint-André / Juri Rappsilber / Nils G Walter / Albert Weixlbaumer /
Abstract: Protein synthesis begins with the formation of a ribosome-messenger RNA (mRNA) complex. In bacteria, the small ribosomal subunit (30) is recruited to many mRNAs through base pairing with the Shine- ...Protein synthesis begins with the formation of a ribosome-messenger RNA (mRNA) complex. In bacteria, the small ribosomal subunit (30) is recruited to many mRNAs through base pairing with the Shine-Dalgarno (SD) sequence and RNA binding by ribosomal protein bS1. Translation can initiate on nascent mRNAs, and RNA polymerase (RNAP) can promote the recruitment of the pioneering 30. Here, we examined 30 recruitment to nascent mRNAs using cryo-electron microscopy, single-molecule fluorescence colocalization, and in-cell cross-linking mass spectrometry. We show that bS1 delivers the mRNA to the ribosome for SD duplex formation and 30 activation. Additionally, bS1 and RNAP stimulate translation initiation. Our work provides a mechanistic framework for how the SD duplex, ribosomal proteins, and RNAP cooperate in 30 recruitment to mRNAs and establish transcription-translation coupling.
History
DepositionSep 18, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51599.png

Downloads & links

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Map

FileDownload / File: emd_51599.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 600 pix.
= 504. Å		0.84 Å/pix.
x 600 pix.
= 504. Å		0.84 Å/pix.
x 600 pix.
= 504. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.229
Minimum - Maximum-0.9608075 - 2.0214233
Average (Standard dev.)0.00041874076 (±0.063038506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 503.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51599_msk_1.map
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AxesZYX

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Additional map: #1

Fileemd_51599_additional_1.map
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Half map: #1

Fileemd_51599_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_51599_half_map_2.map
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Sample components

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Entire : 30S ribosomal subunit

EntireName: 30S ribosomal subunit
Components
  • Complex: 30S ribosomal subunit

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Supramolecule #1: 30S ribosomal subunit

SupramoleculeName: 30S ribosomal subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#24
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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 49.95 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 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:

6ztj

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11965
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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