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- EMDB-35469: Semliki Forest virus VLP in complex with the receptor VLDLR LA1-8... -

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Basic information

Entry
Database: EMDB / ID: EMD-35469
TitleSemliki Forest virus VLP in complex with the receptor VLDLR LA1-8 at 2-fold axis
Map data
Sample
  • Complex: Semliki Forest virus VLP in complex with the receptor VLDLR LA1-8
Biological speciesSemliki Forest virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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_35469.png

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Map

FileDownload / File: emd_35469.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 296 pix.
= 399.6 Å		1.35 Å/pix.
x 296 pix.
= 399.6 Å		1.35 Å/pix.
x 296 pix.
= 399.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.028
Minimum - Maximum-0.16622643 - 0.24984664
Average (Standard dev.)0.00066404644 (±0.01171753)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 399.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35469_half_map_1.map
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Half map: #1

Fileemd_35469_half_map_2.map
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Histogram (log scale)

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Sample components

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Entire : Semliki Forest virus VLP in complex with the receptor VLDLR LA1-8

EntireName: Semliki Forest virus VLP in complex with the receptor VLDLR LA1-8
Components
  • Complex: Semliki Forest virus VLP in complex with the receptor VLDLR LA1-8

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Supramolecule #1: Semliki Forest virus VLP in complex with the receptor VLDLR LA1-8

SupramoleculeName: Semliki Forest virus VLP in complex with the receptor VLDLR LA1-8
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4
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: 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 468868
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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