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- PDB-9e96: WEEV CBA87 VLP in complex with human PCDH10-EC1 -

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Basic information

Entry
Database: PDB / ID: 9.0E+96
TitleWEEV CBA87 VLP in complex with human PCDH10-EC1
Components
  • (Structural polyprotein) x 2
  • Capsid protein
  • Protocadherin-10
KeywordsVIRAL PROTEIN / Alphavirus Receptor
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / homophilic cell adhesion via plasma membrane adhesion molecules / nervous system development / symbiont-mediated suppression of host toll-like receptor signaling pathway / postsynaptic membrane / host cell cytoplasm / cell adhesion / symbiont-mediated suppression of host gene expression / symbiont entry into host cell ...togavirin / T=4 icosahedral viral capsid / homophilic cell adhesion via plasma membrane adhesion molecules / nervous system development / symbiont-mediated suppression of host toll-like receptor signaling pathway / postsynaptic membrane / host cell cytoplasm / cell adhesion / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / calcium ion binding / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / glutamatergic synapse / structural molecule activity / proteolysis / RNA binding / membrane / plasma membrane
Similarity search - Function
Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / : / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein ...Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / : / 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. / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / 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 / Structural polyprotein / Protocadherin-10
Similarity search - Component
Biological speciesWestern equine encephalitis virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.05 Å
AuthorsRaju, S. / Diamond, M.S. / Fremont, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142790 United States
CitationJournal: Cell / Year: 2025
Title: Structural basis for plasticity in receptor engagement by an encephalitic alphavirus.
Authors: Saravanan Raju / Sathvik Palakurty / Alan Sariol / Ngan Wagoner / Lucas J Adams / Sean Hui / William B Klimstra / Daved H Fremont / Michael S Diamond /
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 ...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.
History
DepositionNov 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Structural polyprotein
B: Structural polyprotein
E: Capsid protein
F: Structural polyprotein
G: Structural polyprotein
H: Protocadherin-10
I: Capsid protein
J: Structural polyprotein
K: Structural polyprotein
L: Protocadherin-10
M: Capsid protein
N: Structural polyprotein
O: Structural polyprotein
P: Protocadherin-10
Q: Protocadherin-10
R: Capsid protein


Theoretical massNumber of molelcules
Total (without water)485,27516
Polymers485,27516
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Structural polyprotein / p130


Mass: 47345.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Western equine encephalitis virus / Production host: Homo sapiens (human) / References: UniProt: Q1W679
#2: Protein
Structural polyprotein / p130


Mass: 45393.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Western equine encephalitis virus / Strain: CBA87 / Production host: Homo sapiens (human) / References: UniProt: Q1W679
#3: Protein
Capsid protein / Coat protein / C


Mass: 16712.816 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Western equine encephalitis virus / Production host: Homo sapiens (human) / References: UniProt: P13897, togavirin
#4: Protein
Protocadherin-10


Mass: 11866.213 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCDH10, KIAA1400 / Production host: Homo sapiens (human) / References: UniProt: Q9P2E7
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Western equine encephalitis virus / Type: VIRUS
Details: virus-like particles were produced recombinantly in 293T cells and purified by PEG precipitation followed by density gradient ultracentrifugation.
Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Western equine encephalitis virus / Strain: CBA87
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Passeridae
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
9PHENIX1.21.2model refinement
10ISOLDE1.7.1model refinement
11Coot0.9.8.92model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 231651 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8DEE

8dee


Accession code: 8DEE / Source name: PDB / Type: experimental model
RefinementHighest resolution: 4.05 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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