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Yorodumi- EMDB-20837: Equine spleen apoferritin prepared with the Shake-it-off device -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20837 | |||||||||
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Title | Equine spleen apoferritin prepared with the Shake-it-off device | |||||||||
Map data | apoferritin prepared by the shake-it-off device | |||||||||
Sample |
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Function / homology | Function and homology information intracellular ferritin complex / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Equus caballus (horse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Rubinstein JL / Guo H / Ripstein ZA / Benlekbir S | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Shake-it-off: a simple ultrasonic cryo-EM specimen-preparation device. Authors: John L Rubinstein / Hui Guo / Zev A Ripstein / Ali Haydaroglu / Aaron Au / Christopher M Yip / Justin M Di Trani / Samir Benlekbir / Timothy Kwok / Abstract: Although microscopes and image-analysis software for electron cryomicroscopy (cryo-EM) have improved dramatically in recent years, specimen-preparation methods have lagged behind. Most strategies ...Although microscopes and image-analysis software for electron cryomicroscopy (cryo-EM) have improved dramatically in recent years, specimen-preparation methods have lagged behind. Most strategies still rely on blotting microscope grids with paper to produce a thin film of solution suitable for vitrification. This approach loses more than 99.9% of the applied sample and requires several seconds, leading to problematic air-water interface interactions for macromolecules in the resulting thin film of solution and complicating time-resolved studies. Recently developed self-wicking EM grids allow the use of small volumes of sample, with nanowires on the grid bars removing excess solution to produce a thin film within tens of milliseconds from sample application to freezing. Here, a simple cryo-EM specimen-preparation device that uses components from an ultrasonic humidifier to transfer protein solution onto a self-wicking EM grid is presented. The device is controlled by a Raspberry Pi single-board computer and all components are either widely available or can be manufactured by online services, allowing the device to be constructed in laboratories that specialize in cryo-EM rather than instrument design. The simple open-source design permits the straightforward customization of the instrument for specialized experiments. | |||||||||
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_20837.map.gz | 20.9 MB | EMDB map data format | |
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Header (meta data) | emd-20837-v30.xml emd-20837.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
Images | emd_20837.png | 83.4 KB | ||
Masks | emd_20837_msk_1.map | 22.2 MB | Mask map | |
Others | emd_20837_half_map_1.map.gz emd_20837_half_map_2.map.gz | 20.3 MB 20.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20837 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20837 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20837.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | apoferritin prepared by the shake-it-off device | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 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 | emd_20837_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map B - from cryoSPARC
File | emd_20837_half_map_1.map | ||||||||||||
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Annotation | Half map B - from cryoSPARC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A - from cryoSPARC
File | emd_20837_half_map_2.map | ||||||||||||
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Annotation | Half map A - from cryoSPARC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : apoferritin
Entire | Name: apoferritinFerritin |
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Components |
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-Supramolecule #1: apoferritin
Supramolecule | Name: apoferritin / type: complex / ID: 1 / Parent: 0 Details: purified from equine spleen, commercially available |
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Source (natural) | Organism: Equus caballus (horse) / Organ: Spleen |
Molecular weight | Theoretical: 480 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Support film - topology: HOLEY ARRAY / Support film - Film thickness: 35.0 nm / Pretreatment - Atmosphere: AIR Details: 5 msec spray onto homemade self-wicking copper nanowire grids grown on Cu/Rh 400 mesh grid with 2 micrometer holes spaced 4 micrometer centre-to-centre in sputtered gold. | |||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 40 % / Chamber temperature: 295 K / Details: Experimental Shake-it-off grid freezing device. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 324 / Average exposure time: 30.0 sec. / Average electron dose: 21.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 308752 |
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CTF correction | Software - Name: cryoSPARC (ver. 2) |
Initial angle assignment | Type: OTHER / Software - Name: cryoSPARC (ver. 2) / Details: SGD in cryoSPARC v2 |
Final angle assignment | Type: OTHER / Software - Name: cryoSPARC (ver. 2) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 172469 |