8YW1 | pdb_00008yw1

Semliki Forest virus viron in complex with VLDLR


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into Semiliki forest virus receptor binding modes indicate novel mechanism of virus endocytosis.

Yang, D.Wang, N.Du, B.Sun, Z.Wang, S.He, X.Wang, J.Zheng, T.Chen, Y.Wang, X.Wang, J.

(2024) PLoS Pathog 20: e1012770-e1012770

  • DOI: https://doi.org/10.1371/journal.ppat.1012770
  • Primary Citation of Related Structures:  
    8YVY, 8YVZ, 8YW0, 8YW1, 8YW2

  • PubMed Abstract: 

    The Very Low-Density Lipoprotein Receptor (VLDLR) is an entry receptor for the prototypic alphavirus Semliki Forest Virus (SFV). However, the precise mechanisms underlying the entry of SFV into cells mediated by VLDLR remain unclear. In this study, we found that of the eight class A (LA) repeats of the VLDLR, only LA2, LA3, and LA5 specifically bind to the native SFV virion while synergistically promoting SFV cell attachment and entry. Furthermore, the multiple cryo-electron microscopy structures of VLDLR-SFV complexes and mutagenesis studies have demonstrated that under physiological conditions, VLDLR primarily binds to E1-DIII of site-1, site-2, and site-1' at the twofold symmetry axes of SFV virion through LA2, LA3, and LA5, respectively. These findings unveil a novel mechanism for viral entry mediated by receptors, suggesting that conformational transitions in VLDLR induced by multivalent binding of LAs facilitate cellular internalization of SFV, with significant implications for the design of antiviral therapeutics.


  • Organizational Affiliation
    • State Key Laboratory for Animal Disease Control and Prevention & National Data Center for Animal Infectious Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein E1438Semliki Forest virus 4Mutation(s): 0 
UniProt
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Go to UniProtKB:  P03315
Entity Groups  
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UniProt GroupP03315
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein E2418Semliki Forest virus 4Mutation(s): 0 
UniProt
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Go to UniProtKB:  P03315
Entity Groups  
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UniProt GroupP03315
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Very low-density lipoprotein receptor121Homo sapiensMutation(s): 0 
Gene Names: VLDLR
UniProt & NIH Common Fund Data Resources
Find proteins for P98155 (Homo sapiens)
Explore P98155 
Go to UniProtKB:  P98155
PHAROS:  P98155
GTEx:  ENSG00000147852 
Entity Groups  
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UniProt GroupP98155
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
capsid protein, partial161Semliki Forest virus 4Mutation(s): 0 
UniProt
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Explore P03315 
Go to UniProtKB:  P03315
Entity Groups  
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UniProt GroupP03315
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein E352Semliki Forest virus 4Mutation(s): 0 
UniProt
Find proteins for P03315 (Semliki forest virus)
Explore P03315 
Go to UniProtKB:  P03315
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UniProt GroupP03315
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AB [auth 0],
BB [auth 1],
CB [auth 2],
DB [auth 3],
EB [auth 4],
AB [auth 0],
BB [auth 1],
CB [auth 2],
DB [auth 3],
EB [auth 4],
HA [auth h],
IA [auth i],
JA [auth j],
KA [auth k],
LA [auth l],
MA [auth m],
NA [auth n],
OA [auth o],
PA [auth p],
QA [auth q],
RA [auth r],
SA [auth s],
TA [auth t],
UA [auth u],
VA [auth v],
WA [auth w],
XA [auth x],
YA [auth y],
ZA [auth z]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Data collection, Database references