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- EMDB-12839: E. coli 50S ribosome LiCl core particle, class 5-5 -

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Basic information

Entry
Database: EMDB / ID: EMD-12839
TitleE. coli 50S ribosome LiCl core particle, class 5-5
Map dataSharpened and filtered according to the estimated local resolution
Sample
  • Complex: 50S LiCl core particle, class 1-1
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsLarsson DSD / Selmer M
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Swedish Research Council2017-03827 Sweden
Swedish Research Council2016-06264 Sweden
CitationJournal: Biomolecules / Year: 2022
Title: Structural Consequences of Deproteinating the 50S Ribosome.
Authors: Daniel S D Larsson / Sandesh Kanchugal P / Maria Selmer /
Abstract: Ribosomes are complex ribonucleoprotein particles. Purified 50S ribosomes subjected to high-salt wash, removing a subset of ribosomal proteins (r-proteins), were shown as competent for in vitro ...Ribosomes are complex ribonucleoprotein particles. Purified 50S ribosomes subjected to high-salt wash, removing a subset of ribosomal proteins (r-proteins), were shown as competent for in vitro assembly into functional 50S subunits. Here, we used cryo-EM to determine the structures of such LiCl core particles derived from 50S subunits. A wide range of complexes with large variations in the extent of the ordered 23S rRNA and the occupancy of r-proteins were resolved to between 2.8 Å and 9 Å resolution. Many of these particles showed high similarity to in vivo and in vitro assembly intermediates, supporting the inherent stability or metastability of these states. Similar to states in early ribosome assembly, the main class showed an ordered density for the particle base around the exit tunnel, with domain V and the 3'-half of domain IV disordered. In addition, smaller core particles were discovered, where either domain II or IV was unfolded. Our data support a multi-pathway in vitro disassembly process, similar but reverse to assembly. Dependencies between complex tertiary RNA structures and RNA-protein interactions were observed, where protein extensions dissociated before the globular domains. We observed the formation of a non-native RNA structure upon protein dissociation, demonstrating that r-proteins stabilize native RNA structures and prevent non-native interactions also after folding.
History
DepositionApr 29, 2021-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateDec 14, 2022-
Current statusDec 14, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_12839.png

Downloads & links

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Map

FileDownload / File: emd_12839.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened and filtered according to the estimated local resolution
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 448 pix.
= 479.36 Å		1.07 Å/pix.
x 448 pix.
= 479.36 Å		1.07 Å/pix.
x 448 pix.
= 479.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.55298066 - 1.412584
Average (Standard dev.)5.925053e-05 (±0.020096697)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 479.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_12839_msk_1.map
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Additional map: Unsharpened full map, spherically masked

Fileemd_12839_additional_1.map
AnnotationUnsharpened full map, spherically masked
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Half map: #1

Fileemd_12839_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_12839_half_map_2.map
Projections & Slices
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Sample components

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Entire : 50S LiCl core particle, class 1-1

EntireName: 50S LiCl core particle, class 1-1
Components
  • Complex: 50S LiCl core particle, class 1-1

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Supramolecule #1: 50S LiCl core particle, class 1-1

SupramoleculeName: 50S LiCl core particle, class 1-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Details: 3.5 M LiCl wash, RlmF pull-down, consensus reconstruction
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: JW5107-1

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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

Concentration0.17 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
Details: continuous carbon, 3 microL of sample, incubate for 30 seconds, blot for 3.5 seconds.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsThe sample stage was tilted at 0, 15 or 30 degrees
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 11368 / Average exposure time: 0.77 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 75000
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: OTHER / Details: Ab-initio model in RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 133733
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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