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- EMDB-16400: Contracted cowpea chlorotic mottle virus -

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Basic information

Entry
Database: EMDB / ID: EMD-16400
TitleContracted cowpea chlorotic mottle virus
Map data
Sample
  • Virus: Cowpea chlorotic mottle virus
    • Protein or peptide: Capsid protein
KeywordsIcosahedral / contracted / VIRUS
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
Methodsingle particle reconstruction / cryo EM / Resolution: 1.64 Å
AuthorsHarder OF / Barrass SV / Drabbels M / Lorenz UJ
Funding support Switzerland, European Union, 2 items
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, 2022-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16400.png

Downloads & links

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Map

FileDownload / File: emd_16400.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 768 pix.
= 557.568 Å		0.73 Å/pix.
x 768 pix.
= 557.568 Å		0.73 Å/pix.
x 768 pix.
= 557.568 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.726 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.6969221 - 4.9449453
Average (Standard dev.)0.0013158126 (±0.097145595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 557.568 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16400_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_16400_half_map_2.map
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Sample components

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Entire : Cowpea chlorotic mottle virus

EntireName: Cowpea chlorotic mottle virus
Components
  • Virus: Cowpea chlorotic mottle virus
    • Protein or peptide: Capsid protein

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Supramolecule #1: Cowpea chlorotic mottle virus

SupramoleculeName: Cowpea chlorotic mottle virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12303 / Sci species name: Cowpea chlorotic mottle virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / T number (triangulation number): 3

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Cowpea chlorotic mottle virus
Molecular weightTheoretical: 20.366277 KDa
SequenceString:
MSTVGTGKLT RAQRRAAARK NKRNTRVVQP VIVEPIASGQ GKAIKAWTGY SVSKWTASCA AAEAKVTSAI TISLPNELSS ERNKQLKVG RVLLWLGLLP SVSGTVKSCV TETQTTAAAS FQVALAVADN SKDVVAAMYP EAFKGITLEQ LTADLTIYLY S SAALTEGD VIVHLEVEHV RPTFDDSFTP VY

UniProtKB: Capsid protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureComa free - Residual tilt: 150.0 mrad
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 0.726 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.3 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 273883
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 1.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.1) / Software - details: Homogeneous refinement / Number images used: 169835
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8c38:
Contracted cowpea chlorotic mottle virus

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