+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12531 | |||||||||
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Title | T20S proteasome subtomogram average | |||||||||
Map data | T20S proteasome subtomogram average | |||||||||
Sample |
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Biological species | Thermoplasma acidophilum (acidophilic) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 9.0 Å | |||||||||
Authors | Fernandez JJ | |||||||||
Citation | Journal: J Struct Biol / Year: 2018 Title: Cryo-tomography tilt-series alignment with consideration of the beam-induced sample motion. Authors: Jose-Jesus Fernandez / Sam Li / Tanmay A M Bharat / David A Agard / Abstract: Recent evidence suggests that the beam-induced motion of the sample during tilt-series acquisition is a major resolution-limiting factor in electron cryo-tomography (cryoET). It causes suboptimal ...Recent evidence suggests that the beam-induced motion of the sample during tilt-series acquisition is a major resolution-limiting factor in electron cryo-tomography (cryoET). It causes suboptimal tilt-series alignment and thus deterioration of the reconstruction quality. Here we present a novel approach to tilt-series alignment and tomographic reconstruction that considers the beam-induced sample motion through the tilt-series. It extends the standard fiducial-based alignment approach in cryoET by introducing quadratic polynomials to model the sample motion. The model can be used during reconstruction to yield a motion-compensated tomogram. We evaluated our method on various datasets with different sample sizes. The results demonstrate that our method could be a useful tool to improve the quality of tomograms and the resolution in cryoET. | |||||||||
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_12531.map.gz | 6.2 MB | EMDB map data format | |
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Header (meta data) | emd-12531-v30.xml emd-12531.xml | 7.2 KB 7.2 KB | Display Display | EMDB header |
Images | emd_12531.png | 128.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12531 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12531 | HTTPS FTP |
-Related structure data
Similar structure data | |
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EM raw data | EMPIAR-10651 (Title: CryoET dataset of T20S proteasome for testing motion-aware tilt-series alignment and 3D reconstruction Data size: 5.1 Data #1: Aligned tilt-series of T20S proteasome [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12531.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | T20S proteasome subtomogram average | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.56 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : T20S proteasome
Entire | Name: T20S proteasome |
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Components |
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-Supramolecule #1: T20S proteasome
Supramolecule | Name: T20S proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 14 / Number images used: 3928 |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 3928 |