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- EMDB-63653: Western equine encephalitis virus 71V1658 strain VLP in complex w... -

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Entry
Database: EMDB / ID: EMD-63653
TitleWestern equine encephalitis virus 71V1658 strain VLP in complex with human PCDH10 EC1-6
Map data
Sample
  • Complex: Western equine encephalitis virus 71V1658 strain VLP in complex with human PCDH10 EC1-6
KeywordsWestern equine encephalitis virus / WEEV / 71V1658 strain / receptor / complex / PCDH10 / glycoprotein / VIRAL PROTEIN
Biological speciesWestern equine encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsCao D / Ma B / Cao Z / Ding W / Xu X / Zhang X / Xiang Y
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
National Natural Science Foundation of China (NSFC) China
Chinese Academy of Sciences China
CitationJournal: Cell Rep / Year: 2025
Title: Structural basis for the recognition of two different types of receptors by Western equine encephalitis virus.
Authors: Bingting Ma / Ziyi Cao / Weijia Ding / Xinzheng Zhang / Ye Xiang / Duanfang Cao /
Abstract: Western equine encephalitis virus (WEEV) enters cells via various receptors. Here, we report the cryoelectron microscopy (cryo-EM) structures of WEEV in complex with its receptors PCDH10 and very-low- ...Western equine encephalitis virus (WEEV) enters cells via various receptors. Here, we report the cryoelectron microscopy (cryo-EM) structures of WEEV in complex with its receptors PCDH10 and very-low-density lipoprotein receptor (VLDLR). Structural analysis shows that PCDH10 binds in the cleft formed by adjacent E2-E1 heterodimers of WEEV through its EC1 ectodomain. Residues of viral envelope proteins involved in the interactions with PCDH10 EC1 are unique to WEEV. The strain-specific receptor VLDLR binds WEEV strain McMillan through two consecutive ecto-LDLR class A (LA) repeats. LA1-2, LA2-3, LA3-4, LA4-5, and LA5-6 of VLDLR all have detectable interactions with WEEV. Detailed structures of WEEV in complex with LA1-2 and LA2-3 show that the N-terminal LA repeat binds in the cleft and that the C-terminal LA repeat is attached to the E2 B domain. The acquisition of a single E2 mutation (V265F) allows WEEV strain 71V-1658, originally unable to bind VLDLR, to gain this receptor-binding ability. The binding of VLDLR to WEEV is in a mode different from those of other alphaviruses.
History
DepositionMar 6, 2025-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63653.png

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Map

FileDownload / File: emd_63653.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 220 pix.
= 294.8 Å		1.34 Å/pix.
x 220 pix.
= 294.8 Å		1.34 Å/pix.
x 220 pix.
= 294.8 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
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Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.03243129 - 0.054079253
Average (Standard dev.)0.00021254737 (±0.0024621417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 294.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63653_msk_1.map
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Half map: #1

Fileemd_63653_half_map_1.map
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Half map: #2

Fileemd_63653_half_map_2.map
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Sample components

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Entire : Western equine encephalitis virus 71V1658 strain VLP in complex w...

EntireName: Western equine encephalitis virus 71V1658 strain VLP in complex with human PCDH10 EC1-6
Components
  • Complex: Western equine encephalitis virus 71V1658 strain VLP in complex with human PCDH10 EC1-6

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Supramolecule #1: Western equine encephalitis virus 71V1658 strain VLP in complex w...

SupramoleculeName: Western equine encephalitis virus 71V1658 strain VLP in complex with human PCDH10 EC1-6
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Western equine encephalitis virus

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 1.7 µm / Nominal defocus min: 1.2 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: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56094
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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