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- EMDB-22614: Structure of the Bacterial Ribosome at 2 Angstrom Resolution (50S... -

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Basic information

Entry
Database: EMDB / ID: EMD-22614
TitleStructure of the Bacterial Ribosome at 2 Angstrom Resolution (50S focused refinement)
Map data50S focused refined map
Sample
  • Complex: E. coli 70S ribosome
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.89 Å
AuthorsWatson ZL / Ward FR / Meheust R / Ad O / Schepartz A / Banfield JF / Cate JHD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2021739 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-114454 United States
CitationJournal: Elife / Year: 2020
Title: Structure of the bacterial ribosome at 2 Å resolution.
Authors: Zoe L Watson / Fred R Ward / Raphaël Méheust / Omer Ad / Alanna Schepartz / Jillian F Banfield / Jamie Hd Cate /
Abstract: Using cryo-electron microscopy (cryo-EM), we determined the structure of the 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous positioning of protein and RNA residues, ...Using cryo-electron microscopy (cryo-EM), we determined the structure of the 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous positioning of protein and RNA residues, their detailed chemical interactions, and chemical modifications. Notable features include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former likely conserved in all domains of life. The maps also reveal extensive solvation of the small (30S) ribosomal subunit, and interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The maps and models of the bacterial ribosome presented here now allow a deeper phylogenetic analysis of ribosomal components including structural conservation to the level of solvation. The high quality of the maps should enable future structural analyses of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement.
History
DepositionSep 4, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateOct 7, 2020-
Current statusOct 7, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22614.png

Downloads & links

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Map

FileDownload / File: emd_22614.map.gz / Format: CCP4 / Size: 465.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation50S focused refined map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 496 pix.
= 353.053 Å		0.71 Å/pix.
x 496 pix.
= 353.053 Å		0.71 Å/pix.
x 496 pix.
= 353.053 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7118 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.1710776 - 0.4369476
Average (Standard dev.)-0.0000093292 (±0.013257786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions496496496
Spacing496496496
CellA=B=C: 353.0528 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.711800403225810.711800403225810.71180040322581
M x/y/z496496496
origin x/y/z0.0000.0000.000
length x/y/z353.053353.053353.053
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ510510510
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS496496496
D min/max/mean-0.1710.437-0.000

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Supplemental data

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Half map: 50S focused refined half map 1

Fileemd_22614_half_map_1.map
Annotation50S focused refined half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 50S focused refined half map 2

Fileemd_22614_half_map_2.map
Annotation50S focused refined half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E. coli 70S ribosome

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

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Supramolecule #1: E. coli 70S ribosome

SupramoleculeName: E. coli 70S ribosome / type: complex / ID: 1 / Parent: 0
Details: E. coli 70S ribosome bound to mRNA, tRNAs, and paromomycin
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600
Molecular weightTheoretical: 2.7 MDa

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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

Concentration0.27 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1vy4

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.89 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Ewald sphere corrected in RELION / Number images used: 307495
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4ybb

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