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- EMDB-8802: 80S ribsome from Oryctolagus cuniculus, class I - with non-rotate... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8802 | |||||||||
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Title | 80S ribsome from Oryctolagus cuniculus, class I - with non-rotated/non-swiveled 40S and P site tRNA, derived from EMPIAR-10064 using eClarity | |||||||||
![]() | Rabbit 80S ribosome derived from EMPIAR-10064 using emClarity. Non-rotated/non-swiveled 40S with P site tRNA. | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 9.3 Å | |||||||||
![]() | Himes BA / Zhang P | |||||||||
Funding support | ![]()
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![]() | ![]() Title: emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging. Authors: Benjamin A Himes / Peijun Zhang / ![]() ![]() Abstract: Macromolecular complexes are intrinsically flexible and often challenging to purify for structure determination by single-particle cryo-electron microscopy (cryo-EM). Such complexes can be studied by ...Macromolecular complexes are intrinsically flexible and often challenging to purify for structure determination by single-particle cryo-electron microscopy (cryo-EM). Such complexes can be studied by cryo-electron tomography (cryo-ET) combined with subtomogram alignment and classification, which in exceptional cases achieves subnanometer resolution, yielding insight into structure-function relationships. However, it remains challenging to apply this approach to specimens that exhibit conformational or compositional heterogeneity or are present in low abundance. To address this, we developed emClarity ( https://github.com/bHimes/emClarity/wiki ), a GPU-accelerated image-processing package featuring an iterative tomographic tilt-series refinement algorithm that uses subtomograms as fiducial markers and a 3D-sampling-function-compensated, multi-scale principal component analysis classification method. We demonstrate that our approach offers substantial improvement in the resolution of maps and in the separation of different functional states of macromolecular complexes compared with current state-of-the-art software. | |||||||||
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 | ![]() | 12.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.1 KB 13.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 34.9 KB | Display | ![]() |
Images | ![]() | 144.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8799C ![]() 8803C ![]() 8804C ![]() 8805C ![]() 8806C ![]() 8986C 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 | Rabbit 80S ribosome derived from EMPIAR-10064 using emClarity. Non-rotated/non-swiveled 40S with P site tRNA. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.62 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : 80s ribsome from Oryctolagus cuniculus
Entire | Name: 80s ribsome from Oryctolagus cuniculus |
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Components |
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-Supramolecule #1: 80s ribsome from Oryctolagus cuniculus
Supramolecule | Name: 80s ribsome from Oryctolagus cuniculus / 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
Buffer | pH: 7.6 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: PLASMA CLEANING | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 60 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: blot 3 seconds prior to plunging. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: Gatan Quantum |
Details | Data collection 20 --> -60, 22 --> 60 degrees |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.0037 µm / Nominal defocus min: 0.0024 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |