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- EMDB-11650: M. pneumoniae 70S ribosome in complex with chloramphenicol obtain... -

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Basic information

Entry
Database: EMDB / ID: EMD-11650
TitleM. pneumoniae 70S ribosome in complex with chloramphenicol obtained from in situ data using M
Map data
Sample
  • Complex: 70S ribosome with chloramphenicol
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Methodsubtomogram averaging / cryo EM / Resolution: 3.5 Å
AuthorsTegunov D / Xue L / Dienemann C / Cramer P / Mahamid J
Funding support Germany, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP1935 Germany
European Research Council (ERC)693023 Germany
European Research Council (ERC)760067 Germany
CitationJournal: Nat Methods / Year: 2021
Title: Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells.
Authors: Dimitry Tegunov / Liang Xue / Christian Dienemann / Patrick Cramer / Julia Mahamid /
Abstract: Cryo-electron microscopy (cryo-EM) enables macromolecular structure determination in vitro and inside cells. In addition to aligning individual particles, accurate registration of sample motion and ...Cryo-electron microscopy (cryo-EM) enables macromolecular structure determination in vitro and inside cells. In addition to aligning individual particles, accurate registration of sample motion and three-dimensional deformation during exposures are crucial for achieving high-resolution reconstructions. Here we describe M, a software tool that establishes a reference-based, multi-particle refinement framework for cryo-EM data and couples a comprehensive spatial deformation model to in silico correction of electron-optical aberrations. M provides a unified optimization framework for both frame-series and tomographic tilt-series data. We show that tilt-series data can provide the same resolution as frame-series data on a purified protein specimen, indicating that the alignment step no longer limits the resolution obtainable from tomographic data. In combination with Warp and RELION, M resolves to residue level a 70S ribosome bound to an antibiotic inside intact bacterial cells. Our work provides a computational tool that facilitates structural biology in cells.
History
DepositionAug 22, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateFeb 24, 2021-
Current statusFeb 24, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00412
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.00412
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11650.png

Downloads & links

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Map

FileDownload / File: emd_11650.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 380 pix.
= 323.095 Å		0.85 Å/pix.
x 380 pix.
= 323.095 Å		0.85 Å/pix.
x 380 pix.
= 323.095 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85025 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00412 / Movie #1: 0.00412
Minimum - Maximum-0.00872278 - 0.016820181
Average (Standard dev.)0.00010693552 (±0.0012354465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 323.095 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850250.850250.85025
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z323.095323.095323.095
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0090.0170.000

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Supplemental data

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Mask #1

Fileemd_11650_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Denoised 70S map

Fileemd_11650_additional_1.map
AnnotationDenoised 70S map
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Additional map: Focused on 30S subunit, denoised

Fileemd_11650_additional_2.map
AnnotationFocused on 30S subunit, denoised
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Additional map: Focused on 50S subunit, denoised

Fileemd_11650_additional_3.map
AnnotationFocused on 50S subunit, denoised
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Additional map: Focused on 50S subunit, filtered to local resolution

Fileemd_11650_additional_4.map
AnnotationFocused on 50S subunit, filtered to local resolution
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AxesZYX

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Half map: #2

Fileemd_11650_half_map_1.map
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Half map: #1

Fileemd_11650_half_map_2.map
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Sample components

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Entire : 70S ribosome with chloramphenicol

EntireName: 70S ribosome with chloramphenicol
Components
  • Complex: 70S ribosome with chloramphenicol

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Supramolecule #1: 70S ribosome with chloramphenicol

SupramoleculeName: 70S ribosome with chloramphenicol / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Molecular weightExperimental: 2.7 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 17890
ExtractionNumber tomograms: 65 / Number images used: 24202
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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