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- EMDB-41637: Asymmetric cryoEM reconstruction of Mayaro virus -

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Basic information

Entry
Database: EMDB / ID: EMD-41637
TitleAsymmetric cryoEM reconstruction of Mayaro virus
Map dataAsymmetric MAYV reconstruction
Sample
  • Virus: Mayaro virus
Keywordsalphavirus / cryoEM / enveloped virus / asymmetric / VIRUS
Biological speciesMayaro virus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsChmielewski D / Kaelber J / Jin J / Weaver S / Auguste AJ / Chiu W
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120943 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103832 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI125474 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI153433 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120942 United States
CitationJournal: PNAS Nexus / Year: 2024
Title: Cryogenic electron microscopy and tomography reveal imperfect icosahedral symmetry in alphaviruses.
Authors: David Chmielewski / Guan-Chin Su / Jason T Kaelber / Grigore D Pintilie / Muyuan Chen / Jing Jin / Albert J Auguste / Wah Chiu /
Abstract: Alphaviruses are spherical, enveloped RNA viruses with two-layered icosahedral architecture. The structures of many alphaviruses have been studied using cryogenic electron microscopy (cryo-EM) ...Alphaviruses are spherical, enveloped RNA viruses with two-layered icosahedral architecture. The structures of many alphaviruses have been studied using cryogenic electron microscopy (cryo-EM) reconstructions, which impose icosahedral symmetry on the viral particles. Using cryogenic electron tomography (cryo-ET), we revealed a polarized symmetry defect in the icosahedral lattice of Chikungunya virus (CHIKV) in situ, similar to the late budding particles, suggesting the inherent imperfect symmetry originates from the final pinch-off of assembled virions. We further demonstrated this imperfect symmetry is also present in in vitro purified CHIKV and Mayaro virus, another arthritogenic alphavirus. We employed a subparticle-based single-particle analysis protocol to circumvent the icosahedral imperfection and boosted the resolution of the structure of the CHIKV to ∼3 Å resolution, which revealed detailed molecular interactions between glycoprotein E1-E2 heterodimers in the transmembrane region and multiple lipid-like pocket factors located in a highly conserved hydrophobic pocket. This complementary use of in situ cryo-ET and single-particle cryo-EM approaches provides a more precise structural description of near-icosahedral viruses and valuable insights to guide the development of structure-based antiviral therapies against alphaviruses.
History
DepositionAug 17, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41637.png

Downloads & links

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Map

FileDownload / File: emd_41637.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric MAYV reconstruction
Voxel sizeX=Y=Z: 2 Å
Density
Contour LevelBy AUTHOR: 0.0184
Minimum - Maximum-0.025872285 - 0.039990965
Average (Standard dev.)0.00069593324 (±0.005660651)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 900.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map even

Fileemd_41637_half_map_1.map
AnnotationHalf map even
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map odd

Fileemd_41637_half_map_2.map
AnnotationHalf map odd
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mayaro virus

EntireName: Mayaro virus
Components
  • Virus: Mayaro virus

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Supramolecule #1: Mayaro virus

SupramoleculeName: Mayaro virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 59301 / Sci species name: Mayaro virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Molecular weightTheoretical: 17.596111 KDa
Virus shellShell ID: 1 / Diameter: 700.0 Å / T number (triangulation number): 4

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 35.0 e/Å2

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Image processing

Particle selectionNumber selected: 22314
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22314

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