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Open data
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Basic information
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Title | Subtomogram average of 70S ribosome (50S aligned) | |||||||||
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![]() | 70S / bacterial / RIBOSOME | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 5.8 Å | |||||||||
![]() | Eisenstein F / Danev R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Parallel cryo electron tomography on in situ lamellae. Authors: Fabian Eisenstein / Haruaki Yanagisawa / Hiroka Kashihara / Masahide Kikkawa / Sachiko Tsukita / Radostin Danev / ![]() Abstract: In situ cryo electron tomography of cryo focused ion beam milled samples has emerged in recent years as a powerful technique for structural studies of macromolecular complexes in their native ...In situ cryo electron tomography of cryo focused ion beam milled samples has emerged in recent years as a powerful technique for structural studies of macromolecular complexes in their native cellular environment. However, the possibilities for recording tomographic tilt series in a high-throughput manner are limited, in part by the lamella-shaped samples. Here we utilize a geometrical sample model and optical image shift to record tens of tilt series in parallel, thereby saving time and gaining access to sample areas conventionally used for tracking specimen movement. The parallel cryo electron tomography (PACE-tomo) method achieves a throughput faster than 5 min per tilt series and allows for the collection of sample areas that were previously unreachable, thus maximizing the amount of data from each lamella. Performance testing with ribosomes in vitro and in situ on state-of-the-art and general-purpose microscopes demonstrated the high throughput and quality of PACE-tomo. #1: ![]() Title: Parallel cryo electron tomography on in situ lamellae. Authors: Eisenstein F / Yanagisawa H / Kashihara H / Kikkawa M / Tsukita S / Danev R | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 17.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.9 KB 16.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() ![]() | 7.1 KB 7.1 KB | Display Display | ![]() |
Images | ![]() | 97.1 KB | ||
Masks | ![]() ![]() | 30.5 MB 30.5 MB | ![]() | |
Filedesc metadata | ![]() | 4.6 KB | ||
Others | ![]() ![]() | 15.1 MB 15.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 165.1 KB | Display | ![]() |
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Full document | ![]() | 164.7 KB | Display | |
Data in XML | ![]() | 497 B | Display | |
Data in CIF | ![]() | 373 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article ( |
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EM raw data | ![]() Data size: 222.8 Data #1: Movie frames for all tilt series gain corrected with outdated gain reference [micrographs - multiframe] Data #2: Tilt series and meta data [tilt series]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 2.16 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Mask #2
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-Half map: #2
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-Half map: #1
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Sample components
-Entire : 70S ribosome (50S aligned)
Entire | Name: 70S ribosome (50S aligned) |
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Components |
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-Supramolecule #1: 70S ribosome (50S aligned)
Supramolecule | Name: 70S ribosome (50S aligned) / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | particle |
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Sample preparation
Concentration | 1.8 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | JEOL 2010F |
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Details | Microscope was actually a JEOL JEM-F200 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 2.1 sec. / Average electron dose: 5.4 e/Å2 Details: Tilt series were recorded in parallel using beam image shift |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 40.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.0 µm |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |