+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16798 | |||||||||
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Title | Partially contracted cowpea chlorotic mottle virus | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Icosahedral / partially contracted / virus | |||||||||
Biological species | Cowpea chlorotic mottle virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||
Authors | Harder OF / Barrass SV / Drabbels M / Lorenz UJ | |||||||||
Funding support | Switzerland, European Union, 2 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Fast viral dynamics revealed by microsecond time-resolved cryo-EM. Authors: Oliver F Harder / Sarah V Barrass / Marcel Drabbels / Ulrich J Lorenz / Abstract: Observing proteins as they perform their tasks has largely remained elusive, which has left our understanding of protein function fundamentally incomplete. To enable such observations, we have ...Observing proteins as they perform their tasks has largely remained elusive, which has left our understanding of protein function fundamentally incomplete. To enable such observations, we have recently proposed a technique that improves the time resolution of cryo-electron microscopy (cryo-EM) to microseconds. Here, we demonstrate that microsecond time-resolved cryo-EM enables observations of fast protein dynamics. We use our approach to elucidate the mechanics of the capsid of cowpea chlorotic mottle virus (CCMV), whose large-amplitude motions play a crucial role in the viral life cycle. We observe that a pH jump causes the extended configuration of the capsid to contract on the microsecond timescale. While this is a concerted process, the motions of the capsid proteins involve different timescales, leading to a curved reaction path. It is difficult to conceive how such a detailed picture of the dynamics could have been obtained with any other method, which highlights the potential of our technique. Crucially, our experiments pave the way for microsecond time-resolved cryo-EM to be applied to a broad range of protein dynamics that previously could not have been observed. This promises to fundamentally advance our understanding of protein function. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16798.map.gz | 1.6 GB | EMDB map data format | |
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Header (meta data) | emd-16798-v30.xml emd-16798.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_16798.png | 239 KB | ||
Filedesc metadata | emd-16798.cif.gz | 4.1 KB | ||
Others | emd_16798_half_map_1.map.gz emd_16798_half_map_2.map.gz | 1.6 GB 1.6 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16798 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16798 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16798.map.gz / Format: CCP4 / Size: 1.7 GB / 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: 0.726 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_16798_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16798_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cowpea chlorotic mottle virus
Entire | Name: Cowpea chlorotic mottle virus |
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Components |
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-Supramolecule #1: Cowpea chlorotic mottle virus
Supramolecule | Name: Cowpea chlorotic mottle virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 12303 / Sci species name: Cowpea chlorotic mottle virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Virus shell | Shell ID: 1 / T number (triangulation number): 3 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 4.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.3 µm |
Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Alignment procedure | Coma free - Residual tilt: 150.0 mrad |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 0.726 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 31421 |
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Startup model | Type of model: INSILICO MODEL |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21675 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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