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- EMDB-38378: Structure of Eastern Equine Encephalitis VLP in complex with the ... -

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Entry
Database: EMDB / ID: EMD-38378
TitleStructure of Eastern Equine Encephalitis VLP in complex with the receptor VLDLR LA1-8
Map data
Sample
  • Complex: East Equine Encephalitis virus VLP in complex with its receptor VLDLR LA1-8
KeywordsEast Equine Encephalitis virus / EEEV / receptor / complex / VLDLR / glycoprotein / VIRAL PROTEIN
Biological speciesEastern equine encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCao D / Ma B / Cao Z / 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: Nat Commun / Year: 2024
Title: The receptor VLDLR binds Eastern Equine Encephalitis virus through multiple distinct modes.
Authors: Duanfang Cao / Bingting Ma / Ziyi Cao / Xiaoyu Xu / Xinzheng Zhang / Ye Xiang /
Abstract: Eastern Equine Encephalitis virus (EEEV) is an alphavirus that can cause severe diseases in infected humans. The very low-density lipoprotein receptor (VLDLR) was recently identified as a receptor of ...Eastern Equine Encephalitis virus (EEEV) is an alphavirus that can cause severe diseases in infected humans. The very low-density lipoprotein receptor (VLDLR) was recently identified as a receptor of EEEV. Herein, we performed cryo-electron microscopy structural and biochemistry studies on the specific interactions between EEEV and VLDLR. Our results show that VLDLR binds EEEV at three different sites A, B and C through its membrane-distal LDLR class A (LA) repeats. Site A is located in the cleft in between the E1-E2 heterodimers. Site B is located near the connecting β ribbon of E2 and is in proximity to site A, while site C is on the domain B of E2. The binding of VLDLR LAs to EEEV is in complex modes, including the LA1-2 and LA3-5 mediated two major modes. Disruption of the LA1-2 mediated binding significantly affect the cell attachment of EEEV. However, the mutation W132G of VLDLR impairs the binding of LA3, drives the switch of the binding modes, and significantly enhances the attachment of EEEV to the cell. The W132G variant of VLDLR could be identified in human genome and SNP sequences, implying that people with similar mutations in VLDLR may be highly susceptible to EEEV infection.
History
DepositionDec 19, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateAug 28, 2024-
Current statusAug 28, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38378.png

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Map

FileDownload / File: emd_38378.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 220 pix.
= 297. Å		1.35 Å/pix.
x 220 pix.
= 297. Å		1.35 Å/pix.
x 220 pix.
= 297. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.13360392 - 0.20505281
Average (Standard dev.)0.0008671421 (±0.010828468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_38378_additional_1.map
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AxesZYX

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Half map: #1

Fileemd_38378_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_38378_half_map_2.map
Projections & Slices
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Slices (1/2)
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Sample components

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Entire : East Equine Encephalitis virus VLP in complex with its receptor V...

EntireName: East Equine Encephalitis virus VLP in complex with its receptor VLDLR LA1-8
Components
  • Complex: East Equine Encephalitis virus VLP in complex with its receptor VLDLR LA1-8

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Supramolecule #1: East Equine Encephalitis virus VLP in complex with its receptor V...

SupramoleculeName: East Equine Encephalitis virus VLP in complex with its receptor VLDLR LA1-8
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Eastern 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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (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: 1.7 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 298035
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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