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- EMDB-53908: Composite density map of Semliki Forest virus in complex with Apo... -

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Basic information

Entry
Database: EMDB / ID: EMD-53908
TitleComposite density map of Semliki Forest virus in complex with ApoER2 ligand-binding domain
Map data
Sample
  • Complex: Semliki Forest virus in complex with ApoER2 ligand-binding domain
    • Complex: ApoER2 ligand-binding domain-Fc protein
Keywordscomposite map / Semliki Forest virus / SFV / ApoER2 receptor / localized reconstruction / VIRUS
Biological speciesSemliki Forest virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSong X / Du B / Yang D / Wang J / Huiskonen JT
Funding support Finland, 1 items
OrganizationGrant numberCountry
Jane and Aatos Erkko Foundation Finland
CitationJournal: Nat Commun / Year: 2025
Title: Molecular basis of ApoER2-mediated Semliki Forest virus entry.
Authors: Bingchen Du / Xiyong Song / Bingyu Zhao / Zhibin Shi / Zaisi Liu / Shida Wang / Lili Wei / Xijun He / Juha T Huiskonen / Decheng Yang / Jingfei Wang /
Abstract: The very low-density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2) serve as entry receptors for the Semliki Forest virus (SFV). VLDLR interacts with the SFV E1 domain III ...The very low-density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2) serve as entry receptors for the Semliki Forest virus (SFV). VLDLR interacts with the SFV E1 domain III (DIII) through multiple LDLR class A (LA) domains. However, the ApoER2-mediated SFV entry mechanism remains unclear. Here, we perform biochemical and cellular results and determine the cryogenic electron microscopy (cryo-EM) structures of SFV complexed with ApoER2 LA5 and full-length ApoER2, demonstrating that among the seven LA domains of ApoER2 isoform 1, only LA5 specifically binds to the SFV E1-DIII via a limited interface (353 Ų) and facilitates cell attachment and entry. Site-directed mutagenesis confirms the significance of the residues at the SFV-ApoER2 interface. Significantly, a soluble LA5 decoy receptor neutralizes SFV infection and protects mice from lethal SFV challenge. These findings reveal a LA5-dependent receptor engagement mechanism for SFV entry via ApoER2, distinct from VLDLR.
History
DepositionMay 27, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53908.png

Downloads & links

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Map

FileDownload / File: emd_53908.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 896 pix.
= 860.16 Å		0.96 Å/pix.
x 896 pix.
= 860.16 Å		0.96 Å/pix.
x 896 pix.
= 860.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.02847159 - 0.0664051
Average (Standard dev.)0.00010062075 (±0.0035681592)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions896896896
Spacing896896896
CellA=B=C: 860.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Semliki Forest virus in complex with ApoER2 ligand-binding domain

EntireName: Semliki Forest virus in complex with ApoER2 ligand-binding domain
Components
  • Complex: Semliki Forest virus in complex with ApoER2 ligand-binding domain
    • Complex: ApoER2 ligand-binding domain-Fc protein

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Supramolecule #1: Semliki Forest virus in complex with ApoER2 ligand-binding domain

SupramoleculeName: Semliki Forest virus in complex with ApoER2 ligand-binding domain
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Semliki Forest virus

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Supramolecule #2: ApoER2 ligand-binding domain-Fc protein

SupramoleculeName: ApoER2 ligand-binding domain-Fc protein / type: complex / ID: 2 / Parent: 1
Details: ApoER2 ligand-binding domain in fusion with antibody Fc
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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware: (Name: CTFFIND, RELION) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Scipion / Number images used: 1145346
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION

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