+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4413 | |||||||||
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Title | Tobacco Mosaic Virus | |||||||||
Map data | ||||||||||
Sample |
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Keywords | TMV / helical virus / coat protein / plant pathogen / VIRUS | |||||||||
Function / homology | Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / identical protein binding / Capsid protein Function and homology information | |||||||||
Biological species | Tobacco mosaic virus (strain vulgare) / Tobacco mosaic virus | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
Authors | Song B / Flegler V | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Ultramicroscopy / Year: 2019 Title: Capabilities of the Falcon III detector for single-particle structure determination. Authors: Boyuan Song / Julian Lenhart / Vanessa Judith Flegler / Cihan Makbul / Tim Rasmussen / Bettina Böttcher / Abstract: Direct electron detectors are an essential asset for the resolution revolution in electron cryo microscopy of biological objects. The direct detectors provide two modes of data acquisition; the ...Direct electron detectors are an essential asset for the resolution revolution in electron cryo microscopy of biological objects. The direct detectors provide two modes of data acquisition; the counting mode in which single electrons are counted, and the integrating mode in which the signal that arises from the incident electrons is integrated. While counting mode leads to far higher detective quantum efficiency at all spatial frequencies, the integrating mode enables faster data acquisition at higher exposure rates. For optimal throughput at best possible resolution it is important to understand when the better performance in counting mode becomes essential for solving a structure and when the lower detective quantum efficiency in integrating mode can be compensated by increasing the number of particles in the data set. Here, we provide a case study of the Falcon III camera, which has counting mode capability at exposure rates of <0.9 e/Px² and integrating mode capability at exposure rates above 10 e/Px². We found that counting mode gives better resolution for medium sized complexes such as the β-galactosidase (465 kDa) (2.2 Å, 97% of Nyquist vs. 2.4 Å, 89% of Nyquist) with data sets of similar size. However, for larger particles such as Hepatitis B virus capsid like particles (4.8 MDa) we did not find any resolution gain in counting mode. | |||||||||
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_4413.map.gz | 45.2 MB | EMDB map data format | |
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Header (meta data) | emd-4413-v30.xml emd-4413.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4413_fsc.xml | 21 KB | Display | FSC data file |
Images | emd_4413.png | 199.3 KB | ||
Filedesc metadata | emd-4413.cif.gz | 6.2 KB | ||
Others | emd_4413_half_map_1.map.gz emd_4413_half_map_2.map.gz | 663.8 MB 663.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4413 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4413 | HTTPS FTP |
-Validation report
Summary document | emd_4413_validation.pdf.gz | 373.3 KB | Display | EMDB validaton report |
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Full document | emd_4413_full_validation.pdf.gz | 372.4 KB | Display | |
Data in XML | emd_4413_validation.xml.gz | 26.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4413 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4413 | HTTPS FTP |
-Related structure data
Related structure data | 6i5aMC 4414C 4415C 4416C 4417C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4413.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0635 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_4413_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_4413_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tobacco mosaic virus
Entire | Name: Tobacco mosaic virus |
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Components |
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-Supramolecule #1: Tobacco mosaic virus
Supramolecule | Name: Tobacco mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12243 / Sci species name: Tobacco mosaic virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Nicotiana sp. (plant) |
Molecular weight | Theoretical: 40 MDa |
Virus shell | Shell ID: 1 / Diameter: 180.0 Å |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Tobacco mosaic virus (strain vulgare) / Strain: vulgare |
Molecular weight | Theoretical: 17.636621 KDa |
Sequence | String: MSYSITTPSQ FVFLSSAWAD PIELINLCTN ALGNQFQTQQ ARTVVQRQFS EVWKPSPQVT VRFPDSDFKV YRYNAVLDPL VTALLGAFD TRNRIIEVEN QANPTTAETL DATRRVDDAT VAIRSAINNL IVELIRGTGS YNRSSFESSS GLVWTSGPAT UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Quantifoil 400 mesh copper grids R 1.2/1.3 were used (Quantifoil Micro Tools GmbH, Jena, Germany). Grids were glow discharged in air at a pressure of 2.2x10-2 Torr for 2 min at medium power ...Details: Quantifoil 400 mesh copper grids R 1.2/1.3 were used (Quantifoil Micro Tools GmbH, Jena, Germany). Grids were glow discharged in air at a pressure of 2.2x10-2 Torr for 2 min at medium power with a Harrick Plasma cleaner (PDC-002). Subsequently, 3-4 ul of the sample was pipetted onto the glow discharged grids and plunge frozen in liquid Ethane with a Vitrobot IV (FEI). The sample chamber of the Vitrobot was maintained at 4C and 100% humidity. Wait time between sample application and blotting was 45 s, the drain time 0 s, the blot time 3 s and the blot force 0.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 79.0 K / Max: 80.0 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1001 / Average exposure time: 5.0 sec. / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.12 µm / Calibrated defocus min: 0.58 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / 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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 105 |
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Output model | PDB-6i5a: |