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- EMDB-22877: E. coli ribosome structure -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-22877
TitleE. coli ribosome structure
Map dataE. coli ribosome structure
Sample
  • Complex: subtomogram average structure of E. coli ribosome
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 Å
AuthorsChang YJ / Liu J / Xiang YJ / Jacobs-Wagner C
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI087946 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI132818 United States
CitationJournal: Cell / Year: 2021
Title: Interconnecting solvent quality, transcription, and chromosome folding in Escherichia coli.
Authors: Yingjie Xiang / Ivan V Surovtsev / Yunjie Chang / Sander K Govers / Bradley R Parry / Jun Liu / Christine Jacobs-Wagner /
Abstract: All cells fold their genomes, including bacterial cells, where the chromosome is compacted into a domain-organized meshwork called the nucleoid. How compaction and domain organization arise is not ...All cells fold their genomes, including bacterial cells, where the chromosome is compacted into a domain-organized meshwork called the nucleoid. How compaction and domain organization arise is not fully understood. Here, we describe a method to estimate the average mesh size of the nucleoid in Escherichia coli. Using nucleoid mesh size and DNA concentration estimates, we find that the cytoplasm behaves as a poor solvent for the chromosome when the cell is considered as a simple semidilute polymer solution. Monte Carlo simulations suggest that a poor solvent leads to chromosome compaction and DNA density heterogeneity (i.e., domain formation) at physiological DNA concentration. Fluorescence microscopy reveals that the heterogeneous DNA density negatively correlates with ribosome density within the nucleoid, consistent with cryoelectron tomography data. Drug experiments, together with past observations, suggest the hypothesis that RNAs contribute to the poor solvent effects, connecting chromosome compaction and domain formation to transcription and intracellular organization.
History
DepositionOct 20, 2020-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateJan 11, 2023-
Current statusJan 11, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22877.png

Downloads & links

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Map

FileDownload / File: emd_22877.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. coli ribosome structure
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.46 Å/pix.
x 72 pix.
= 392.904 Å		5.46 Å/pix.
x 72 pix.
= 392.904 Å		5.46 Å/pix.
x 72 pix.
= 392.904 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.457 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.15
Minimum - Maximum-0.32799274 - 0.64050084
Average (Standard dev.)6.918362e-07 (±0.089359954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 392.904 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.4575.4575.457
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z392.904392.904392.904
α/β/γ90.00090.00090.000
start NX/NY/NZ161360275
NX/NY/NZ300237246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS727272
D min/max/mean-0.3280.6410.000

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Supplemental data

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Sample components

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Entire : subtomogram average structure of E. coli ribosome

EntireName: subtomogram average structure of E. coli ribosome
Components
  • Complex: subtomogram average structure of E. coli ribosome

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Supramolecule #1: subtomogram average structure of E. coli ribosome

SupramoleculeName: subtomogram average structure of E. coli ribosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.2
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 5028
ExtractionNumber tomograms: 1 / Number images used: 5028
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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