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- EMDB-11999: M. pneumoniae 70S ribosome in complex with chloramphenicol obtain... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11999 | |||||||||||||||
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Title | M. pneumoniae 70S ribosome in complex with chloramphenicol obtained from in situ data using M, focused refinement of 50S sub-unit | |||||||||||||||
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Function / homology | ![]() large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome ...large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 3.4 Å | |||||||||||||||
![]() | Tegunov D / Xue L / Dienemann C / Cramer P / Mahamid J | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 191.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.8 KB 12.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13 KB | Display | ![]() |
Images | ![]() | 85.2 KB | ||
Masks | ![]() | 166.4 MB | ![]() | |
Others | ![]() ![]() | 156.7 MB 156.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 466.5 KB | Display | ![]() |
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Full document | ![]() | 465.6 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oodM C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 83.8 Data #1: Unaligned tilt movies of M. pneumoniae [tilt series]) ![]() Data size: 67.8 Data #1: 50S templates of Mycoplasma pneumoniae used for 2D and 3D template matching [reconstructed volumes] Data #2: Single-exposure micrographs of untilted Mycoplasma pneumoniae cells [micrographs - single frame] Data #3: Tomographic tilt series of Mycoplasma pneumoniae cells [tilt series] Data #4: Tomographic reconstructions of Mycoplasma pneumoniae cells [reconstructed volumes]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.8502 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11999_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11999_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : 70S ribosome with chloramphenicol
Entire | Name: 70S ribosome with chloramphenicol |
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Components |
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-Supramolecule #1: 70S ribosome with chloramphenicol
Supramolecule | Name: 70S ribosome with chloramphenicol / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 2.7 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 120.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |