9E9Z | pdb_00009e9z

SINV-WEEV Fleming in complex with VLDLR LA(1-2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for plasticity in receptor engagement by an encephalitic alphavirus.

Raju, S.Palakurty, S.Sariol, A.Wagoner, N.Adams, L.J.Hui, S.Klimstra, W.B.Fremont, D.H.Diamond, M.S.

(2025) Cell 188: 2943

  • DOI: https://doi.org/10.1016/j.cell.2025.02.036
  • Primary Citation of Related Structures:  
    9E96, 9E9Y, 9E9Z, 9EAU

  • PubMed Abstract: 

    The structural basis for shifts in receptor usage remains poorly understood despite the implications for virus adaptation and emergence. Western equine encephalitis virus (WEEV) strains exhibit different patterns of engagement for two of their entry receptors: very-low-density lipoprotein receptor (VLDLR) and protocadherin 10 (PCDH10). Using structural and functional studies, we show that while all WEEV strains have a lipoprotein class A (LA) domain binding site near the E1 fusion loop, VLDLR engagement requires a second binding site in E2 that can vary with single nucleotide substitutions. We also resolve a structure of PCDH10 bound to WEEV, which reveals interactions near the E1 fusion loop with residues that also mediate LA domain binding. Evolutionary analysis enabled the generation of a PCDH10 decoy that protects in vivo against all WEEV strains tested. Our experiments demonstrate how viruses can engage multiple receptors using shared determinants, which likely impacts cellular tropism and virulence.


  • Organizational Affiliation
    • Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Structural polyprotein
A, C, G, J
439Western equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for A0A5J6NBQ1 (Western equine encephalitis virus)
Explore A0A5J6NBQ1 
Go to UniProtKB:  A0A5J6NBQ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5J6NBQ1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Structural polyprotein
B, D, H, K
408Western equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for A0A5J6NBQ1 (Western equine encephalitis virus)
Explore A0A5J6NBQ1 
Go to UniProtKB:  A0A5J6NBQ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5J6NBQ1
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein
E, F, I, L
153Western equine encephalitis virusMutation(s): 0 
EC: 3.4.21.90
UniProt
Find proteins for P13897 (Western equine encephalitis virus)
Explore P13897 
Go to UniProtKB:  P13897
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UniProt GroupP13897
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Very low-density lipoprotein receptorM [auth V],
N [auth W],
O [auth X],
P [auth Y]
78Homo 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI143673

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-05-14
    Changes: Data collection
  • Version 1.2: 2025-06-11
    Changes: Data collection, Database references
  • Version 1.3: 2025-09-10
    Changes: Data collection, Structure summary