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- PDB-8c38: Contracted cowpea chlorotic mottle virus -

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Basic information

Entry
Database: PDB / ID: 8c38
TitleContracted cowpea chlorotic mottle virus
ComponentsCapsid protein
KeywordsVIRUS / Icosahedral / contracted
Function / homologyBromovirus 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 speciesCowpea chlorotic mottle virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.64 Å
AuthorsHarder, O.F. / Barrass, S.V. / Drabbels, M. / Lorenz, U.J.
Funding support Switzerland, European Union, 2items
OrganizationGrant numberCountry
Swiss National Science FoundationPP00P2_163681 Switzerland
European Research Council (ERC)759145European Union
CitationJournal: 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
DepositionDec 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Capsid protein
D: Capsid protein
I: Capsid protein


Theoretical massNumber of molelcules
Total (without water)61,0993
Polymers61,0993
Non-polymers00
Water00
1
C: Capsid protein
D: Capsid protein
I: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,665,930180
Polymers3,665,930180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation59

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Components

#1: Protein Capsid protein / CP / Coat 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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cowpea chlorotic mottle virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Cowpea chlorotic mottle virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Virus shellTriangulation number (T number): 3
Buffer solutionpH: 5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Residual tilt: 150 mradians
Image recordingElectron dose: 0.726 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.4/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
EM software
IDNameVersionCategoryDetails
1cryoSPARC4.0.1particle selectionTemplate picker
4cryoSPARC4.0.1CTF correctionPatch CTF
7ISOLDE1.0.4model fitting
12cryoSPARC4.0.13D reconstructionHomogeneous refinement
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 273883
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 1.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 169835 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL

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