+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33118 | |||||||||
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Title | In situ subtomogram average of 80S ribosome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | in situ / 80S / eukaryotic / RIBOSOME | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 8.2 Å | |||||||||
Authors | Eisenstein F / Danev R | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: Nat Methods / Year: 2023 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: Journal: Biorxiv / Year: 2022 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 | emd_33118.map.gz | 70.6 MB | EMDB map data format | |
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Header (meta data) | emd-33118-v30.xml emd-33118.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33118_fsc.xml | 11.5 KB | Display | FSC data file |
Images | emd_33118.png | 121.2 KB | ||
Masks | emd_33118_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-33118.cif.gz | 4.2 KB | ||
Others | emd_33118_half_map_1.map.gz emd_33118_half_map_2.map.gz | 61.4 MB 61.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33118 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33118 | HTTPS FTP |
-Validation report
Summary document | emd_33118_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_33118_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_33118_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_33118_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33118 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33118 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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EM raw data | EMPIAR-10987 (Title: Parallel cryo electron tomography (PACE-tomo) of 80S ribosomes in situ Data size: 132.3 Data #1: Gain corrected movie frames for all tilt series [micrographs - multiframe] Data #2: Tilt series and meta data [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33118.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.64 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33118_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33118_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_33118_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 80S ribosome in situ
Entire | Name: 80S ribosome in situ |
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Components |
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-Supramolecule #1: 80S ribosome in situ
Supramolecule | Name: 80S ribosome in situ / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mus musculus (house mouse) / Strain: EpH4 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Homemade / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 80 % / Chamber temperature: 310 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average exposure time: 0.5 sec. / Average electron dose: 3.55 e/Å2 Details: Tilt series were recorded in parallel using beam image shift |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |