9E96 | pdb_00009e96

WEEV CBA87 VLP in complex with human PCDH10-EC1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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 polyproteinA,
D [auth F],
H [auth J],
L [auth N]
439Western equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for Q1W679 (Western equine encephalitis virus)
Explore Q1W679 
Go to UniProtKB:  Q1W679
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1W679
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Structural polyproteinB,
E [auth G],
I [auth K],
M [auth O]
408Western equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for Q1W679 (Western equine encephalitis virus)
Explore Q1W679 
Go to UniProtKB:  Q1W679
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1W679
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid proteinC [auth E],
G [auth I],
K [auth M],
P [auth R]
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
Protocadherin-10F [auth H],
J [auth L],
N [auth P],
O [auth Q]
104Homo sapiensMutation(s): 0 
Gene Names: PCDH10KIAA1400
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2E7 (Homo sapiens)
Explore Q9P2E7 
Go to UniProtKB:  Q9P2E7
PHAROS:  Q9P2E7
GTEx:  ENSG00000138650 
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UniProt GroupQ9P2E7
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2
MODEL REFINEMENTISOLDE1.7.1
MODEL REFINEMENTCoot0.9.8.92

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 StatesU19 AI142790

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Data collection, Database references
  • Version 1.2: 2025-08-27
    Changes: Data collection, Structure summary