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- EMDB-49104: WEEV McMillan VLP in complex with VLDLR-LBD-Fc ASU -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-49104
TitleWEEV McMillan VLP in complex with VLDLR-LBD-Fc ASU
Map data
Sample
  • Virus: Western equine encephalitis virus
KeywordsAlphavirus / lipoprotein / VIRAL PROTEIN
Biological speciesWestern equine encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.51 Å
AuthorsRaju S / Diamond MS / Fremont DH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142790 United States
CitationJournal: Cell / Year: 2025
Title: Structural basis for plasticity in receptor engagement by an encephalitic alphavirus.
Authors: Saravanan Raju / Sathvik Palakurty / Alan Sariol / Ngan Wagoner / Lucas J Adams / Sean Hui / William B Klimstra / Daved H Fremont / Michael S Diamond /
Abstract: The structural basis for shifts in receptor usage remains poorly understood despite the implications for virus adaptation and emergence. Western equine encephalitis virus (WEEV) strains exhibit ...The structural basis for shifts in receptor usage remains poorly understood despite the implications for virus adaptation and emergence. Western equine encephalitis virus (WEEV) strains exhibit different patterns of engagement for two of their entry receptors: very-low-density lipoprotein receptor (VLDLR) and protocadherin 10 (PCDH10). Using structural and functional studies, we show that while all WEEV strains have a lipoprotein class A (LA) domain binding site near the E1 fusion loop, VLDLR engagement requires a second binding site in E2 that can vary with single nucleotide substitutions. We also resolve a structure of PCDH10 bound to WEEV, which reveals interactions near the E1 fusion loop with residues that also mediate LA domain binding. Evolutionary analysis enabled the generation of a PCDH10 decoy that protects in vivo against all WEEV strains tested. Our experiments demonstrate how viruses can engage multiple receptors using shared determinants, which likely impacts cellular tropism and virulence.
History
DepositionFeb 7, 2025-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49104.png

Downloads & links

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Map

FileDownload / File: emd_49104.map.gz / Format: CCP4 / Size: 103 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.)
1.08 Å/pix.
x 300 pix.
= 324.3 Å		1.08 Å/pix.
x 300 pix.
= 324.3 Å		1.08 Å/pix.
x 300 pix.
= 324.3 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.081 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.6978041 - 1.1362429
Average (Standard dev.)0.0009807198 (±0.056570582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49104_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_49104_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Western equine encephalitis virus

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

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Supramolecule #1: Western equine encephalitis virus

SupramoleculeName: Western equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11039 / Sci species name: Western equine encephalitis virus / 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106235
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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