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Yorodumi- EMDB-11998: M. pneumoniae 70S ribosome in complex with chloramphenicol obtain... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11998 | |||||||||||||||
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Title | M. pneumoniae 70S ribosome in complex with chloramphenicol obtained from in situ data using M, focused refinement of 30S sub-unit | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Function / homology | Function and homology information ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) | |||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 3.7 Å | |||||||||||||||
Authors | Tegunov D / Xue L / Dienemann C / Cramer P / Mahamid J | |||||||||||||||
Funding support | Germany, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11998.map.gz | 191.5 MB | EMDB map data format | |
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Header (meta data) | emd-11998-v30.xml emd-11998.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11998_fsc.xml | 13 KB | Display | FSC data file |
Images | emd_11998.png | 85.2 KB | ||
Masks | emd_11998_msk_1.map | 166.4 MB | Mask map | |
Others | emd_11998_half_map_1.map.gz emd_11998_half_map_2.map.gz | 85.4 MB 85.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11998 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11998 | HTTPS FTP |
-Validation report
Summary document | emd_11998_validation.pdf.gz | 466.7 KB | Display | EMDB validaton report |
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Full document | emd_11998_full_validation.pdf.gz | 465.9 KB | Display | |
Data in XML | emd_11998_validation.xml.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11998 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11998 | HTTPS FTP |
-Related structure data
Related structure data | 7oocM C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10499 (Title: Tilt series of native M. pneumoniae cells treated with chloramphenicol Data size: 83.8 Data #1: Unaligned tilt movies of M. pneumoniae [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11998.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85025 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11998_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11998_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11998_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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: Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) |
Molecular weight | Experimental: 2.7 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |