9EAU | pdb_00009eau

RRV DKTA VLP in complex with VLDLR-LBD-Fc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 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
Spike glycoprotein E1A,
D [auth E],
G [auth I],
J [auth M]
438Ross river virus (STRAIN T48)Mutation(s): 4 
UniProt
Find proteins for C9DZM3 (Ross River virus)
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Go to UniProtKB:  C9DZM3
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UniProt GroupC9DZM3
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein E2B,
E [auth F],
H [auth J],
K [auth N]
419Ross river virus (STRAIN T48)Mutation(s): 0 
UniProt
Find proteins for Q076B2 (Ross River virus)
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Go to UniProtKB:  Q076B2
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UniProt GroupQ076B2
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid proteinC,
F [auth G],
I [auth K],
L [auth O]
158Ross river virus (STRAIN T48)Mutation(s): 0 
EC: 3.4.21.90
UniProt
Find proteins for P08491 (Ross river virus (strain T48))
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Go to UniProtKB:  P08491
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UniProt GroupP08491
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Very low-density lipoprotein receptorM [auth Y],
N [auth Z]
39Homo 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 
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UniProt GroupP98155
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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