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Yorodumi- EMDB-10707: Anabaena sp. PCC 7120 Septal Junction Average from Manually Mille... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10707 | |||||||||
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Title | Anabaena sp. PCC 7120 Septal Junction Average from Manually Milled Lamellae | |||||||||
Map data | Septal junction average generated from 343 particles and 5-fold symmetrizing. Lamellae were generated in using a manual FIB milling approach. | |||||||||
Sample |
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Biological species | Nostoc sp. PCC 7120 (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 30.0 Å | |||||||||
Authors | Zachs T / Pilhofer M | |||||||||
Funding support | Switzerland, European Union, 2 items
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Citation | Journal: Elife / Year: 2020 Title: Fully automated, sequential focused ion beam milling for cryo-electron tomography. Authors: Tobias Zachs / Andreas Schertel / João Medeiros / Gregor L Weiss / Jannik Hugener / Joao Matos / Martin Pilhofer / Abstract: Cryo-electron tomography (cryoET) has become a powerful technique at the interface of structural biology and cell biology, due to its unique ability for imaging cells in their native state and ...Cryo-electron tomography (cryoET) has become a powerful technique at the interface of structural biology and cell biology, due to its unique ability for imaging cells in their native state and determining structures of macromolecular complexes in their cellular context. A limitation of cryoET is its restriction to relatively thin samples. Sample thinning by cryo-focused ion beam (cryoFIB) milling has significantly expanded the range of samples that can be analyzed by cryoET. Unfortunately, cryoFIB milling is low-throughput, time-consuming and manual. Here, we report a method for fully automated sequential cryoFIB preparation of high-quality lamellae, including rough milling and polishing. We reproducibly applied this method to eukaryotic and bacterial model organisms, and show that the resulting lamellae are suitable for cryoET imaging and subtomogram averaging. Since our method reduces the time required for lamella preparation and minimizes the need for user input, we envision the technique will render previously inaccessible projects feasible. | |||||||||
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_10707.map.gz | 273 KB | EMDB map data format | |
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Header (meta data) | emd-10707-v30.xml emd-10707.xml | 7.7 KB 7.7 KB | Display Display | EMDB header |
Images | emd_10707.png | 61.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10707 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10707 | HTTPS FTP |
-Validation report
Summary document | emd_10707_validation.pdf.gz | 225 KB | Display | EMDB validaton report |
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Full document | emd_10707_full_validation.pdf.gz | 224.1 KB | Display | |
Data in XML | emd_10707_validation.xml.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10707 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10707 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10376 (Title: Yeast Tilt Series Collected on Lamella Generated by Fully Automated FIB Milling Data size: 2.6 Data #1: Yeast Tilt Series Collected on Lamella Generated by Fully Automated FIB Milling [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10707.map.gz / Format: CCP4 / Size: 333 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Septal junction average generated from 343 particles and 5-fold symmetrizing. Lamellae were generated in using a manual FIB milling approach. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.757 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 : Septal Junction
Entire | Name: Septal Junction |
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Components |
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-Supramolecule #1: Septal Junction
Supramolecule | Name: Septal Junction / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Nostoc sp. PCC 7120 (bacteria) |
-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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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 343 |
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Extraction | Number tomograms: 9 / Number images used: 343 |
Final angle assignment | Type: OTHER |