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Yorodumi- EMDB-22350: CryoEM structure of human light chain apoferritin calculated from... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22350 | |||||||||
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Title | CryoEM structure of human light chain apoferritin calculated from EER movies (intra-fraction motion correction experiment, 1.5x supersampling, particle motion corrected without B-spline interpolation | |||||||||
Map data | Sharpened map | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.1 Å | |||||||||
Authors | Guo H / Rubinstein J | |||||||||
Funding support | Canada, 2 items
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Citation | Journal: IUCrJ / Year: 2020 Title: Electron-event representation data enable efficient cryoEM file storage with full preservation of spatial and temporal resolution. Authors: Hui Guo / Erik Franken / Yuchen Deng / Samir Benlekbir / Garbi Singla Lezcano / Bart Janssen / Lingbo Yu / Zev A Ripstein / Yong Zi Tan / John L Rubinstein / Abstract: Direct detector device (DDD) cameras have revolutionized electron cryomicroscopy (cryoEM) with their high detective quantum efficiency (DQE) and output of movie data. A high ratio of camera frame ...Direct detector device (DDD) cameras have revolutionized electron cryomicroscopy (cryoEM) with their high detective quantum efficiency (DQE) and output of movie data. A high ratio of camera frame rate (frames per second) to camera exposure rate (electrons per pixel per second) allows electron counting, which further improves the DQE and enables the recording of super-resolution information. Movie output also allows the correction of specimen movement and compensation for radiation damage. However, these movies come at the cost of producing large volumes of data. It is common practice to sum groups of successive camera frames to reduce the final frame rate, and therefore the file size, to one suitable for storage and image processing. This reduction in the temporal resolution of the camera requires decisions to be made during data acquisition that may result in the loss of information that could have been advantageous during image analysis. Here, experimental analysis of a new electron-event representation (EER) data format for electron-counting DDD movies is presented, which is enabled by new hardware developed by Thermo Fisher Scientific for their Falcon DDD cameras. This format enables the recording of DDD movies at the raw camera frame rate without sacrificing either spatial or temporal resolution. Experimental data demonstrate that the method retains super-resolution information and allows the correction of specimen movement at the physical frame rate of the camera while maintaining manageable file sizes. The EER format will enable the development of new methods that can utilize the full spatial and temporal resolution of DDD cameras. #1: Journal: Biorxiv / Year: 2020 Title: Electron Event Representation (EER) data enables efficient cryoEM file storage with full preservation of spatial and temporal resolution Authors: Guo H / Franken E / Deng Y / Benlekbir S / Lezcano GS / Janssen B / Yu L / Ripstein ZA / Tan YZ / Rubinstein JL | |||||||||
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_22350.map.gz | 201.9 MB | EMDB map data format | |
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Header (meta data) | emd-22350-v30.xml emd-22350.xml | 31.7 KB 31.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22350_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_22350.png | 144.2 KB | ||
Masks | emd_22350_msk_1.map | 216 MB | Mask map | |
Others | emd_22350_additional_1.map.gz emd_22350_additional_2.map.gz emd_22350_additional_3.map.gz emd_22350_additional_4.map.gz emd_22350_additional_5.map.gz emd_22350_additional_6.map.gz emd_22350_half_map_1.map.gz emd_22350_half_map_2.map.gz | 202.5 MB 202.2 MB 202.4 MB 202.2 MB 202.3 MB 202.2 MB 164.9 MB 164.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22350 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22350 | HTTPS FTP |
-Validation report
Summary document | emd_22350_validation.pdf.gz | 78.8 KB | Display | EMDB validaton report |
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Full document | emd_22350_full_validation.pdf.gz | 77.9 KB | Display | |
Data in XML | emd_22350_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22350 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22350 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10474 (Title: EER movies of human light chain apoferritin / Data size: 642.1 Data #1: Falcon3 EER movies of human light chain apoferritin at 75000 nominal magnification used for intra-fraction motion correction experiment [micrographs - multiframe] Data #2: Falcon4 EER movies of human light chain apoferritin at 47000 nominal magnification used for super-resolution experiment [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22350.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.70667 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_22350_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Map calculated from EER frames corresponding to 0-0.7 e/A^2 exposure
File | emd_22350_additional_1.map | ||||||||||||
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Annotation | Map calculated from EER frames corresponding to 0-0.7 e/A^2 exposure | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map calculated from EER frames corresponding to 0.7-1.4...
File | emd_22350_additional_2.map | ||||||||||||
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Annotation | Map calculated from EER frames corresponding to 0.7-1.4 e/A^2 exposure | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map calculated from EER frames corresponding to 1.4-2.1...
File | emd_22350_additional_3.map | ||||||||||||
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Annotation | Map calculated from EER frames corresponding to 1.4-2.1 e/A^2 exposure | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map calculated from EER frames corresponding to 2.1-2.8...
File | emd_22350_additional_4.map | ||||||||||||
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Annotation | Map calculated from EER frames corresponding to 2.1-2.8 e/A^2 exposure | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map calculated from EER frames corresponding to 2.8-3.5...
File | emd_22350_additional_5.map | ||||||||||||
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Annotation | Map calculated from EER frames corresponding to 2.8-3.5 e/A^2 exposure | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map calculated from EER frames corresponding to 3.5-4.2...
File | emd_22350_additional_6.map | ||||||||||||
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Annotation | Map calculated from EER frames corresponding to 3.5-4.2 e/A^2 exposure | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_22350_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_22350_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human light chain apoferritin
Entire | Name: Human light chain apoferritin |
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Components |
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-Supramolecule #1: Human light chain apoferritin
Supramolecule | Name: Human light chain apoferritin / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F |
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 | 10 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Homemade / Material: COPPER/RHODIUM / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 30.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 325 / Average exposure time: 60.0 sec. / Average electron dose: 41.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 1.6 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |