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- EMDB-35471: Semliki Forest virus VLP in complex with the receptor VLDLR LA2-3 -

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Basic information

Entry
Database: EMDB / ID: EMD-35471
TitleSemliki Forest virus VLP in complex with the receptor VLDLR LA2-3
Map dataOverall density map of SFV VLP in complex with VLDLR LA2-3
Sample
  • Complex: Semliki Forest virus VLP in complex with the receptor VLDLR LA2-3
Biological speciesSemliki Forest virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsCao D / Ma B / Cao Z / 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 / Year: 2023
Title: Structure of Semliki Forest virus in complex with its receptor VLDLR.
Authors: Duanfang Cao / Bingting Ma / Ziyi Cao / Xinzheng Zhang / Ye Xiang /
Abstract: Semliki Forest virus (SFV) is an alphavirus that uses the very-low-density lipoprotein receptor (VLDLR) as a receptor during infection of its vertebrate hosts and insect vectors. Herein, we used ...Semliki Forest virus (SFV) is an alphavirus that uses the very-low-density lipoprotein receptor (VLDLR) as a receptor during infection of its vertebrate hosts and insect vectors. Herein, we used cryoelectron microscopy to study the structure of SFV in complex with VLDLR. We found that VLDLR binds multiple E1-DIII sites of SFV through its membrane-distal LDLR class A (LA) repeats. Among the LA repeats of the VLDLR, LA3 has the best binding affinity to SFV. The high-resolution structure shows that LA3 binds SFV E1-DIII through a small surface area of 378 Å, with the main interactions at the interface involving salt bridges. Compared with the binding of single LA3s, consecutive LA repeats around LA3 promote synergistic binding to SFV, during which the LAs undergo a rotation, allowing simultaneous key interactions at multiple E1-DIII sites on the virion and enabling the binding of VLDLRs from divergent host species to SFV.
History
DepositionFeb 26, 2023-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35471.png

Downloads & links

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Map

FileDownload / File: emd_35471.map.gz / Format: CCP4 / Size: 759.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall density map of SFV VLP in complex with VLDLR LA2-3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 584 pix.
= 788.4 Å		1.35 Å/pix.
x 584 pix.
= 788.4 Å		1.35 Å/pix.
x 584 pix.
= 788.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0075
Minimum - Maximum-0.014227523 - 0.02982103
Average (Standard dev.)0.0012552445 (±0.0026833152)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions584584584
Spacing584584584
CellA=B=C: 788.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Density map of SFV VLP in complex with VLDLR LA2-3 at the 2-fold axis

Fileemd_35471_additional_1.map
AnnotationDensity map of SFV VLP in complex with VLDLR LA2-3 at the 2-fold axis
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Density map of SFV VLP in complex with VLDLR LA2-3 at the 5-fold axis

Fileemd_35471_additional_2.map
AnnotationDensity map of SFV VLP in complex with VLDLR LA2-3 at the 5-fold axis
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35471_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35471_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 : Semliki Forest virus VLP in complex with the receptor VLDLR LA2-3

EntireName: Semliki Forest virus VLP in complex with the receptor VLDLR LA2-3
Components
  • Complex: Semliki Forest virus VLP in complex with the receptor VLDLR LA2-3

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Supramolecule #1: Semliki Forest virus VLP in complex with the receptor VLDLR LA2-3

SupramoleculeName: Semliki Forest virus VLP in complex with the receptor VLDLR LA2-3
type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Semliki Forest 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: DIRECT ELECTRON DE-16 (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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15216
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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