+Open data
-Basic information
Entry | Database: PDB / ID: 8cpy | |||||||||
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Title | Extended cowpea chlorotic mottle virus | |||||||||
Components | Capsid protein | |||||||||
Keywords | VIRUS / Icosahedral / extended | |||||||||
Function / homology | Bromovirus coat protein / Bromovirus coat protein / T=3 icosahedral viral capsid / viral nucleocapsid / ribonucleoprotein complex / structural molecule activity / RNA binding / Capsid protein Function and homology information | |||||||||
Biological species | Cowpea chlorotic mottle virus | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Harder, O.F. / Barrass, S.V. / Drabbels, M. / Lorenz, U.J. | |||||||||
Funding support | Switzerland, European Union, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cpy.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cpy.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 8cpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cpy_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8cpy_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8cpy_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 8cpy_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/8cpy ftp://data.pdbj.org/pub/pdb/validation_reports/cp/8cpy | HTTPS FTP |
-Related structure data
Related structure data | 16790MC 8c38C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 20366.277 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Cowpea chlorotic mottle virus / References: UniProt: P03601 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cowpea chlorotic mottle virus / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Cowpea chlorotic mottle virus |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Virus shell | Triangulation number (T number): 3 |
Buffer solution | pH: 4.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Extended CCMV was prepared at pH 7.6 and incubated with NPE-caged-proton in a 6:1 ratio prior to plunge freezing. The grid was then irritated in a Linkam Cryo-stage with a UV laser, ...Details: Extended CCMV was prepared at pH 7.6 and incubated with NPE-caged-proton in a 6:1 ratio prior to plunge freezing. The grid was then irritated in a Linkam Cryo-stage with a UV laser, activating the NPE-caged-proton and reducing the sample pH to 4.5. |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 900 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Residual tilt: 150 mradians |
Image recording | Electron dose: 0.726 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
EM imaging optics | Energyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 139274 | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30095 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||
Atomic model building | Source name: PDB / Type: experimental model |