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- EMDB-43376: CryoET of VSV incubated with liposomes at pH 5.5 -

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Basic information

Entry
Database: EMDB / ID: EMD-43376
TitleCryoET of VSV incubated with liposomes at pH 5.5
Map dataTomogram TS7092 from the 150s post-incubation dataset, pertaining to Fig.2C.
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: To be Published
Title: Capturing Intermediates and Membrane Remodeling during Class III Fusion
Authors: Milojevic L / Si Z / Xia X / Chen L / He Y / Tang S / Luo M / Zhou ZH
History
DepositionJan 15, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43376.png

Downloads & links

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Map

FileDownload / File: emd_43376.map.gz / Format: CCP4 / Size: 581.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram TS7092 from the 150s post-incubation dataset, pertaining to Fig.2C.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.16 Å/pix.
x 233 pix.
= 1901.28 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-6.0494914 - 19.690193000000001
Average (Standard dev.)0.4787837 (±0.3822037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions960682233
Spacing682960233
CellA: 5565.12 Å / B: 7833.5996 Å / C: 1901.2799 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: 27

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