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- EMDB-23358: Structure of E. coli 70S ribosome from EMPIAR-10304 at 4.8 Angstr... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23358 | |||||||||
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Title | Structure of E. coli 70S ribosome from EMPIAR-10304 at 4.8 Angstrom Resolution | |||||||||
![]() | Structure of E. coli 70S ribosome from EMPIAR-10304 at 4.8 Angstrom Resolution | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 4.8 Å | |||||||||
![]() | Bouvette J / Liu HF / Du X / Zhou Y / Sikkema AP / Mello JFR / Klemm B / Huang R / Schaaper RM / Borgnia MJ / Bartesaghi A | |||||||||
![]() | ![]() Title: Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography. Authors: Jonathan Bouvette / Hsuan-Fu Liu / Xiaochen Du / Ye Zhou / Andrew P Sikkema / Juliana da Fonseca Rezende E Mello / Bradley P Klemm / Rick Huang / Roel M Schaaper / Mario J Borgnia / Alberto Bartesaghi / ![]() Abstract: Tomographic reconstruction of cryopreserved specimens imaged in an electron microscope followed by extraction and averaging of sub-volumes has been successfully used to derive atomic models of ...Tomographic reconstruction of cryopreserved specimens imaged in an electron microscope followed by extraction and averaging of sub-volumes has been successfully used to derive atomic models of macromolecules in their biological environment. Eliminating biochemical isolation steps required by other techniques, this method opens up the cell to in-situ structural studies. However, the need to compensate for errors in targeting introduced during mechanical navigation of the specimen significantly slows down tomographic data collection thus limiting its practical value. Here, we introduce protocols for tilt-series acquisition and processing that accelerate data collection speed by up to an order of magnitude and improve map resolution compared to existing approaches. We achieve this by using beam-image shift to multiply the number of areas imaged at each stage position, by integrating geometrical constraints during imaging to achieve high precision targeting, and by performing per-tilt astigmatic CTF estimation and data-driven exposure weighting to improve final map resolution. We validated our beam image-shift electron cryo-tomography (BISECT) approach by determining the structure of a low molecular weight target (~300 kDa) at 3.6 Å resolution where density for individual side chains is clearly resolved. | |||||||||
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 | ![]() | 8.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.5 KB 15.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 76.3 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Others | ![]() ![]() ![]() | 54.8 MB 32.7 MB 32.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of E. coli 70S ribosome from EMPIAR-10304 at 4.8 Angstrom Resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.1 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 | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Structure of E. coli 70S ribosome from EMPIAR-10304...
File | emd_23358_additional_1.map | ||||||||||||
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Annotation | Structure of E. coli 70S ribosome from EMPIAR-10304 at 4.8 Angstrom Resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Structure of E. coli 70S ribosome from EMPIAR-10304...
File | emd_23358_half_map_1.map | ||||||||||||
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Annotation | Structure of E. coli 70S ribosome from EMPIAR-10304 at 4.8 Angstrom Resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Structure of E. coli 70S ribosome from EMPIAR-10304...
File | emd_23358_half_map_2.map | ||||||||||||
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Annotation | Structure of E. coli 70S ribosome from EMPIAR-10304 at 4.8 Angstrom Resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : 70S ribosome
Entire | Name: 70S ribosome |
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Components |
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-Supramolecule #1: 70S ribosome
Supramolecule | Name: 70S ribosome / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 |
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 K3 (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Average electron dose: 3.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |