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- EMDB-46612: Subtomogram average of the ribonucleoprotein of the rabies virus ... -

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Basic information

Entry
Database: EMDB / ID: EMD-46612
TitleSubtomogram average of the ribonucleoprotein of the rabies virus CVS-27 strain
Map data
Sample
  • Virus: Lyssavirus rabies
KeywordsRhabdoviruses / Rabies virus / Wild-type / CryoET / VIRAL PROTEIN
Biological speciesLyssavirus rabies
Methodsubtomogram averaging / cryo EM / Resolution: 18.7 Å
AuthorsZhou ZH / Cai X / Zhou K / Alvarez-Cabrera AL / Si Z / Wang H / He Y / Li C
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI094386 United States
CitationJournal: Viruses / Year: 2024
Title: Structural Heterogeneity of the Rabies Virus Virion.
Authors: Xiaoying Cai / Kang Zhou / Ana Lucia Alvarez-Cabrera / Zhu Si / Hui Wang / Yao He / Cally Li / Z Hong Zhou /
Abstract: Rabies virus (RABV) is among the first recognized viruses of public health concern and has historically contributed to the development of viral vaccines. Despite these significances, the three- ...Rabies virus (RABV) is among the first recognized viruses of public health concern and has historically contributed to the development of viral vaccines. Despite these significances, the three-dimensional structure of the RABV virion remains unknown due to the challenges in isolating structurally homogenous virion samples in sufficient quantities needed for structural investigation. Here, by combining the capabilities of cryogenic electron tomography (cryoET) and microscopy (cryoEM), we determined the three-dimensional structure of the wild-type RABV virion. Tomograms of RABV virions reveal a high level of structural heterogeneity among the bullet-shaped virion particles encompassing the glycoprotein (G) trimer-decorated envelope and the nucleocapsid composed of RNA, nucleoprotein (N), and matrix protein (M). The structure of the trunk region of the virion was determined by cryoEM helical reconstruction, revealing a one-start N-RNA helix bound by a single layer of M proteins at an N:M ratio of 1. The N-M interaction differs from that in fellow rhabdovirus vesicular stomatitis virus (VSV), which features two layers of M stabilizing the N-RNA helix at an M:N ratio of 2. These differences in both M-N stoichiometry and binding allow RABV to flex its N-RNA helix more freely and point to different mechanisms of viral assembly between these two bullet-shaped rhabdoviruses.
History
DepositionAug 16, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46612.png

Downloads & links

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Map

FileDownload / File: emd_46612.map.gz / Format: CCP4 / Size: 3.4 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.)
4.08 Å/pix.
x 96 pix.
= 391.68 Å		4.08 Å/pix.
x 96 pix.
= 391.68 Å		4.08 Å/pix.
x 96 pix.
= 391.68 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 4.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.012610851 - 0.024638262
Average (Standard dev.)0.002172232 (±0.0038342173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 391.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46612_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_46612_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46612_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Lyssavirus rabies

EntireName: Lyssavirus rabies
Components
  • Virus: Lyssavirus rabies

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Supramolecule #1: Lyssavirus rabies

SupramoleculeName: Lyssavirus rabies / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11292 / Sci species name: Lyssavirus rabies / Sci species strain: CVS-27 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 18.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 2300
ExtractionNumber tomograms: 10 / Number images used: 7534
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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