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- EMDB-53903: Semliki Forest virus trimer 2 in complex with ApoER2 LA5 -

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Basic information

Entry
Database: EMDB / ID: EMD-53903
TitleSemliki Forest virus trimer 2 in complex with ApoER2 LA5
Map data
Sample
  • Complex: Semliki Forest virus in complex with ApoER2 LA5
    • Complex: ApoER2 LA5-Fc protein
    • Protein or peptide: Protein E3
    • Protein or peptide: Capsid protein
  • Protein or peptide: Structural polyprotein
  • Protein or peptide: Envelope glycoprotein E2
KeywordsSemliki Forest virus / SFV / ApoER2 receptor / localized reconstruction / VIRUS
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell ...togavirin / T=4 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein / Frameshifted structural polyprotein
Similarity search - Component
Biological speciesSemliki Forest virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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_53903.png

Downloads & links

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Map

FileDownload / File: emd_53903.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0045
Minimum - Maximum-0.032933507 - 0.06821128
Average (Standard dev.)0.00025048232 (±0.003094909)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53903_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_53903_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_53903_half_map_2.map
Projections & Slices
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Sample components

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Entire : Semliki Forest virus in complex with ApoER2 LA5

EntireName: Semliki Forest virus in complex with ApoER2 LA5
Components
  • Complex: Semliki Forest virus in complex with ApoER2 LA5
    • Complex: ApoER2 LA5-Fc protein
    • Protein or peptide: Protein E3
    • Protein or peptide: Capsid protein
  • Protein or peptide: Structural polyprotein
  • Protein or peptide: Envelope glycoprotein E2

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Supramolecule #1: Semliki Forest virus in complex with ApoER2 LA5

SupramoleculeName: Semliki Forest virus in complex with ApoER2 LA5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #4
Source (natural)Organism: Semliki Forest virus

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Supramolecule #2: ApoER2 LA5-Fc protein

SupramoleculeName: ApoER2 LA5-Fc protein / type: complex / ID: 2 / Parent: 1 / Details: ApoER2 LA5 in fusion with antibody Fc
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein E3

MacromoleculeName: Protein E3 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus
Molecular weightTheoretical: 7.384484 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString:
SAPLITAMCV LANATFPCFQ PPCVPCCYEN NAEATLRMLE DNVDRPGYYD LLQAALTCRN GTRHRR

UniProtKB: Frameshifted structural polyprotein

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Macromolecule #2: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus
Molecular weightTheoretical: 47.489766 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCRHDHA SAYKAHTASL KAKVRVMYGN VNQTVDVYVN GDHAVTIGGT Q FIFGPLSS ...String:
YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCRHDHA SAYKAHTASL KAKVRVMYGN VNQTVDVYVN GDHAVTIGGT Q FIFGPLSS AWTPFDNKIV VYKDEVFNQD FPPYGSGQPG RFGDIQSRTV ESNDLYANTA LKLARPSPGM VHVPYTQTPS GF KYWLKEK GTALNTKAPF GCQIKTNPVR AMNCAVGNIP VSMNLPDSAF TRIVEAPTII DLTCTVATCT HSSDFGGVLT LTY KTDKNG DCSVHSHSNV ATLQEATAKV KTAGKVTLHF STASASPSFV VSLCSARATC SASCEPPKDH IVPYAASHSN VVFP DMSGT ALSWVQKISG GLGAFAIGAI LVLVVVTCIG LRR

UniProtKB: Structural polyprotein

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Macromolecule #3: Envelope glycoprotein E2

MacromoleculeName: Envelope glycoprotein E2 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Semliki Forest virus
Molecular weightTheoretical: 46.870277 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: SVSQHFNVYK ATRPYIAYCA DCGAGHSCHS PVAIEAVRSE ATDGMLKIQF SAQIGIDKSD NHDYTKIRYA DGHAIENAVR SSLKVATSG DCFVHGTMGH FILAKCPPGE FLQVSIQDTR NAVRACRIQY HHDPQPVGRE KFTIRPHYGK EIPCTTYQQT T AKTVEEID ...String:
SVSQHFNVYK ATRPYIAYCA DCGAGHSCHS PVAIEAVRSE ATDGMLKIQF SAQIGIDKSD NHDYTKIRYA DGHAIENAVR SSLKVATSG DCFVHGTMGH FILAKCPPGE FLQVSIQDTR NAVRACRIQY HHDPQPVGRE KFTIRPHYGK EIPCTTYQQT T AKTVEEID MHMPPDTPDR TLLSQQSGNV KITVGGKKVK YNCTCGTGNV GTTNSDMTIN TCLIEQCHVS VTDHKKWQFN SP FVPRADE PARKGKVHIP FPLDNITCRV PMAREPTVIH GKREVTLHLH PDHPTLFSYR TLGEDPQYHE EWVTAAVERT IPV PVDGME YHWGNNDPVR LWSQLTTEGK PHGWPHQIVQ YYYGLYPAAT VSAVVGMSLL ALISIFASCY MLVAARSKCL TPYA LTPGA AVPWTLGILC CAPRAHA

UniProtKB: Frameshifted structural polyprotein

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Macromolecule #4: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Semliki Forest virus
Molecular weightTheoretical: 29.920711 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: MNYIPTQTFY GRRWRPRPAA RPWPLQATPV APVVPDFQAQ QMQQLISAVN ALTMRQNAIA PARPPKPKKK KTTKPKPKTQ PKKINGKTQ QQKKKDKQAD KKKKKPGKRE RMCMKIENDC IFEVKHEGKV TGYACLVGDK VMKPAHVKGV IDNADLAKLA F KKSSKYDL ...String:
MNYIPTQTFY GRRWRPRPAA RPWPLQATPV APVVPDFQAQ QMQQLISAVN ALTMRQNAIA PARPPKPKKK KTTKPKPKTQ PKKINGKTQ QQKKKDKQAD KKKKKPGKRE RMCMKIENDC IFEVKHEGKV TGYACLVGDK VMKPAHVKGV IDNADLAKLA F KKSSKYDL ECAQIPVHMR SDASKYTHEK PEGHYNWHHG AVQYSGGRFT IPTGAGKPGD SGRPIFDNKG RVVAIVLGGA NE GSRTALS VVTWNKDMVT RVTPEGSEEW

UniProtKB: Frameshifted structural polyprotein

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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: GATAN K3 (6k 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: 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: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 611068
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
FSC plot (resolution estimation)

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