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- EMDB-44551: Map of eastern equine encephalitis virus q3 spike protein in comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-44551
TitleMap of eastern equine encephalitis virus q3 spike protein in complex with VLDLR without masked refinement
Map data
Sample
  • Virus: Eastern equine encephalitis virus
    • Complex: EEEV strain PE6 mature glycoprotein E1
    • Complex: EEEV strain PE6 mature glycoprotein E2
    • Complex: EEEV strain PE6 mature glycoprotein E3
    • Complex: EEEV strain PE6 mature capsid protein
    • Complex: VLDLR
KeywordsAlphaviruses / Receptor / VIRUS LIKE PARTICLE
Biological speciesEastern equine encephalitis virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsAbraham J / Yang P / Li W / Fan X / Pan J
Funding support United States, 1 items
OrganizationGrant numberCountry
Burroughs Wellcome Fund United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for VLDLR recognition by eastern equine encephalitis virus.
Authors: Pan Yang / Wanyu Li / Xiaoyi Fan / Junhua Pan / Colin J Mann / Haley Varnum / Lars E Clark / Sarah A Clark / Adrian Coscia / Himanish Basu / Katherine Nabel Smith / Vesna Brusic / Jonathan Abraham /
Abstract: Eastern equine encephalitis virus (EEEV) is the most virulent alphavirus that infects humans, and many survivors develop neurological sequelae, including paralysis and intellectual disability. ...Eastern equine encephalitis virus (EEEV) is the most virulent alphavirus that infects humans, and many survivors develop neurological sequelae, including paralysis and intellectual disability. Alphavirus spike proteins comprise trimers of heterodimers of glycoproteins E2 and E1 that mediate binding to cellular receptors and fusion of virus and host cell membranes during entry. We recently identified very-low density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2) as cellular receptors for EEEV and a distantly related alphavirus, Semliki Forest virus (SFV). Here, we use single-particle cryo-electron microscopy (cryo-EM) to determine structures of the EEEV and SFV spike glycoproteins bound to the VLDLR ligand-binding domain and found that EEEV and SFV interact with the same cellular receptor through divergent binding modes. Our studies suggest that the ability of LDLR-related proteins to interact with viral spike proteins through very small footprints with flexible binding modes results in a low evolutionary barrier to the acquisition of LDLR-related proteins as cellular receptors for diverse sets of viruses.
History
DepositionApr 21, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44551.png

Downloads & links

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Map

FileDownload / File: emd_44551.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.0066646882 - 0.01102863
Average (Standard dev.)0.00011611215 (±0.0011940561)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_44551_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44551_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44551_half_map_2.map
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
    • Complex: EEEV strain PE6 mature glycoprotein E1
    • Complex: EEEV strain PE6 mature glycoprotein E2
    • Complex: EEEV strain PE6 mature glycoprotein E3
    • Complex: EEEV strain PE6 mature capsid protein
    • Complex: VLDLR

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Supramolecule #1: Eastern equine encephalitis virus

SupramoleculeName: Eastern equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / NCBI-ID: 11021 / Sci species name: Eastern equine encephalitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Supramolecule #2: EEEV strain PE6 mature glycoprotein E1

SupramoleculeName: EEEV strain PE6 mature glycoprotein E1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Eastern equine encephalitis virus

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Supramolecule #3: EEEV strain PE6 mature glycoprotein E2

SupramoleculeName: EEEV strain PE6 mature glycoprotein E2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Eastern equine encephalitis virus

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Supramolecule #4: EEEV strain PE6 mature glycoprotein E3

SupramoleculeName: EEEV strain PE6 mature glycoprotein E3 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Eastern equine encephalitis virus

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Supramolecule #5: EEEV strain PE6 mature capsid protein

SupramoleculeName: EEEV strain PE6 mature capsid protein / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Eastern equine encephalitis virus

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Supramolecule #6: VLDLR

SupramoleculeName: VLDLR / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #5 / Details: EEEV receptor VLDLR
Source (natural)Organism: Homo sapiens (human)

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

22276

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 776700
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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