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- EMDB-66645: Structure of the vesicular stomatitis virus nucleocapsid subbox -

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Basic information

Entry
Database: EMDB / ID: EMD-66645
TitleStructure of the vesicular stomatitis virus nucleocapsid subbox
Map data
Sample
  • Virus: Vesicular stomatitis Indiana virus
KeywordsVSV / RNP / nucleocapsid / VIRAL PROTEIN
Biological speciesVesicular stomatitis Indiana virus
Methodsubtomogram averaging / cryo EM / Resolution: 4.6 Å
AuthorsLiu K / Zhang J / Li S
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)#32241031 China
National Natural Science Foundation of China (NSFC)#82241066 China
National Natural Science Foundation of China (NSFC)#32171195 China
CitationJournal: Nat Commun / Year: 2026
Title: FlyTomo: a streamlined software for on-the-fly cryo-ET data processing and diagnosis.
Authors: Zheyuan Zhang / Cheng Peng / Weiping Zhang / Jiaming Liang / Kexin Liu / Yong Chen / Junxia Zhang / Rui Liang / Yutong Song / Sai Li /
Abstract: Cryo-ET combined with subtomogram averaging (STA) enables the structural elucidation of macromolecular assemblies in native environments. However, their widespread adoption has been limited by the ...Cryo-ET combined with subtomogram averaging (STA) enables the structural elucidation of macromolecular assemblies in native environments. However, their widespread adoption has been limited by the labor-intensive, expertise-dependent data processing workflow. Here we present FlyTomo, a software that streamlines data processing from frame alignment to STA with high-throughput for authentic cryo-ET scenarios. During data acquisition, FlyTomo performs real-time diagnosis, enabling prompt feedback on sample quality, microscope performance and structural features. After acquisition, it aggregates diagnostic metrics into an overview, guiding users through data review and refinement. FlyTomo also curates raw and processed data into directories to simplify data management and archiving. We validate FlyTomo across a diverse set of authentic cryo-ET samples, including purified enveloped viruses and cryo-lamellae, on multiple microscopes and cameras, achieving structures at resolutions of 3.4 to 7.3 Å. Collectively, by integrating accuracy, scalability and usability, FlyTomo reduces the technical barrier for in situ structural biology using cryo-ET.
History
DepositionOct 17, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66645.png

Downloads & links

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Map

FileDownload / File: emd_66645.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 160 pix.
= 217.44 Å		1.36 Å/pix.
x 160 pix.
= 217.44 Å		1.36 Å/pix.
x 160 pix.
= 217.44 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.359 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-9.884475999999999 - 12.754925999999999
Average (Standard dev.)-0.0000014962096 (±0.71440476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 217.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66645_msk_1.map
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Half map: #2

Fileemd_66645_half_map_1.map
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Half map: #1

Fileemd_66645_half_map_2.map
Projections & Slices
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Sample components

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Entire : Vesicular stomatitis Indiana virus

EntireName: Vesicular stomatitis Indiana virus
Components
  • Virus: Vesicular stomatitis Indiana virus

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Supramolecule #1: Vesicular stomatitis Indiana virus

SupramoleculeName: Vesicular stomatitis Indiana virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 11277 / Sci species name: Vesicular stomatitis Indiana virus / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 5.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 21937
ExtractionNumber tomograms: 122 / Number images used: 147 / Software - Name: IMOD
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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