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- EMDB-43382: CryoET of VSV incubated with liposomes at pH 5.5 -

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Basic information

Entry
Database: EMDB / ID: EMD-43382
TitleCryoET of VSV incubated with liposomes at pH 5.5
Map dataTomogram TS7106 from the 150s post-incubation dataset, pertaining to Fig.7M.
Sample
  • Virus: Vesicular stomatitis Indiana virus strain San Juan
KeywordsVirus / Liposome / Fusion / Class III Fusion / VSV / VSV G
Biological speciesVesicular stomatitis Indiana virus strain San Juan
Methodelectron tomography / cryo EM
AuthorsSi Z / Xia X / Tang S / Milojevic L
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI171426 United States
CitationJournal: Sci Adv / Year: 2024
Title: Capturing intermediates and membrane remodeling in class III viral fusion.
Authors: Lenka Milojević / Zhu Si / Xian Xia / Lauren Chen / Yao He / Sijia Tang / Ming Luo / Z Hong Zhou /
Abstract: Enveloped viruses enter cells by fusing their envelopes to host cell membranes. Vesicular stomatitis virus (VSV) glycoprotein (G) is a prototype for class III fusion proteins. Although structures of ...Enveloped viruses enter cells by fusing their envelopes to host cell membranes. Vesicular stomatitis virus (VSV) glycoprotein (G) is a prototype for class III fusion proteins. Although structures of the stable pre- and postfusion ectodomain of G are known, its fusogenic intermediates are insufficiently characterized. Here, we incubated VSV virions with late endosome-mimicking liposomes at pH 5.5 and used cryo-electron tomography (cryo-ET) to visualize stages of VSV's membrane fusion pathway, capture refolding intermediates of G, and reconstruct a sequence of G conformational changes. We observe that the G trimer disassembles into monomers and parallel dimers that explore a broad conformational space. Extended intermediates engage target membranes and mediate fusion, resulting in viral uncoating and linearization of the ribonucleoprotein genome. These viral fusion intermediates provide mechanistic insights into class III viral fusion processes, opening avenues for future research and structure-based design of fusion inhibition-based antiviral therapeutics.
History
DepositionJan 15, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43382.png

Downloads & links

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Map

FileDownload / File: emd_43382.map.gz / Format: CCP4 / Size: 499.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram TS7106 from the 150s post-incubation dataset, pertaining to Fig.7M.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.16 Å/pix.
x 200 pix.
= 1632. Å		8.16 Å/pix.
x 960 pix.
= 7833.6 Å		8.16 Å/pix.
x 682 pix.
= 5565.12 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 8.16 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-8.365883 - 27.956800000000001
Average (Standard dev.)0.479913 (±0.5218739)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions960682200
Spacing682960200
CellA: 5565.12 Å / B: 7833.5996 Å / C: 1632.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Vesicular stomatitis Indiana virus strain San Juan

EntireName: Vesicular stomatitis Indiana virus strain San Juan
Components
  • Virus: Vesicular stomatitis Indiana virus strain San Juan

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Supramolecule #1: Vesicular stomatitis Indiana virus strain San Juan

SupramoleculeName: Vesicular stomatitis Indiana virus strain San Juan / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11285
Sci species name: Vesicular stomatitis Indiana virus strain San Juan
Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 5.5
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Support film - Material: CARBON / Support film - topology: LACEY
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Cell Microscopy Core, Department of Cell Biology, University Medical Center Utrecht
Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 41

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