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- EMDB-42187: Eastern equine encephalitis virus (PE-6) VLP (icosahedral) -

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Basic information

Entry
Database: EMDB / ID: EMD-42187
TitleEastern equine encephalitis virus (PE-6) VLP (icosahedral)
Map dataEEEV PE-6 VLP icosahedral reconstruction
Sample
  • Virus: Eastern equine encephalitis virus
Keywordsvirus / VIRUS LIKE PARTICLE
Biological speciesEastern equine encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsAdams LJ / Fremont DH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell / Year: 2024
Title: Structural and functional basis of VLDLR usage by Eastern equine encephalitis virus.
Authors: Lucas J Adams / Saravanan Raju / Hongming Ma / Theron Gilliland / Douglas S Reed / William B Klimstra / Daved H Fremont / Michael S Diamond /
Abstract: The very-low-density lipoprotein receptor (VLDLR) comprises eight LDLR type A (LA) domains and supports entry of distantly related alphaviruses, including Eastern equine encephalitis virus (EEEV) and ...The very-low-density lipoprotein receptor (VLDLR) comprises eight LDLR type A (LA) domains and supports entry of distantly related alphaviruses, including Eastern equine encephalitis virus (EEEV) and Semliki Forest virus (SFV). Here, by resolving multiple cryo-electron microscopy structures of EEEV-VLDLR complexes and performing mutagenesis and functional studies, we show that EEEV uses multiple sites (E1/E2 cleft and E2 A domain) to engage more than one LA domain simultaneously. However, no single LA domain is necessary or sufficient to support efficient EEEV infection. Whereas all EEEV strains show conservation of two VLDLR-binding sites, the EEEV PE-6 strain and a few other EEE complex members feature a single amino acid substitution that enables binding of LA domains to an additional site on the E2 B domain. These structural and functional analyses informed the design of a minimal VLDLR decoy receptor that neutralizes EEEV infection and protects mice from lethal challenge.
History
DepositionOct 4, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42187.png

Downloads & links

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Map

FileDownload / File: emd_42187.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEEEV PE-6 VLP icosahedral reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 720 pix.
= 778.32 Å		1.08 Å/pix.
x 720 pix.
= 778.32 Å		1.08 Å/pix.
x 720 pix.
= 778.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.081 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.15784897 - 0.33991146
Average (Standard dev.)0.0013509324 (±0.024606166)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 778.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: EEEV PE-6 VLP icosahedral reconstruction (unsharpened)

Fileemd_42187_additional_1.map
AnnotationEEEV PE-6 VLP icosahedral reconstruction (unsharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EEEV PE-6 VLP icosahedral reconstruction (half map A)

Fileemd_42187_half_map_1.map
AnnotationEEEV PE-6 VLP icosahedral reconstruction (half map A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EEEV PE-6 VLP icosahedral reconstruction (half map B)

Fileemd_42187_half_map_2.map
AnnotationEEEV PE-6 VLP icosahedral reconstruction (half map B)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Eastern equine encephalitis virus

EntireName: Eastern equine encephalitis virus
Components
  • Virus: Eastern equine encephalitis virus

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Supramolecule #1: Eastern equine encephalitis virus

SupramoleculeName: Eastern equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11021 / Sci species name: Eastern equine encephalitis virus / Sci species strain: PE-6 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 37.93 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41227
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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