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- PDB-9dqy: Structure of western equine encephalitis virus Imperial 181 VLP i... -

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Basic information

Entry
Database: PDB / ID: 9dqy
TitleStructure of western equine encephalitis virus Imperial 181 VLP in complex with house sparrow PCDH10 EC1
Components
  • Cadherin domain-containing protein
  • Spike glycoprotein E1
  • Structural polyprotein
KeywordsVIRUS LIKE PARTICLE / western equine encephalitis virus / WEEV / receptor binding / PCDH10 / virus like particles
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / host cell endoplasmic reticulum / homophilic cell-cell adhesion / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell ...togavirin / T=4 icosahedral viral capsid / host cell endoplasmic reticulum / homophilic cell-cell adhesion / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / calcium ion binding / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / host cell nucleus / virion membrane / structural molecule activity / proteolysis / RNA binding / plasma membrane
Similarity search - Function
Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / : / Cadherin conserved site / Cadherin domain signature. / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein ...Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / : / Cadherin conserved site / Cadherin domain signature. / 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-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
Cadherin domain-containing protein / Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesWestern equine encephalitis virus
Passer domesticus (house sparrow)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsAbraham, J. / Fan, X. / Li, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2025
Title: Molecular basis for shifted receptor recognition by an encephalitic arbovirus.
Authors: Xiaoyi Fan / Wanyu Li / Jessica Oros / Jessica A Plante / Brooke M Mitchell / Jesse S Plung / Himanish Basu / Sivapratha Nagappan-Chettiar / Joshua M Boeckers / Laurentia V Tjang / Colin J ...Authors: Xiaoyi Fan / Wanyu Li / Jessica Oros / Jessica A Plante / Brooke M Mitchell / Jesse S Plung / Himanish Basu / Sivapratha Nagappan-Chettiar / Joshua M Boeckers / Laurentia V Tjang / Colin J Mann / Vesna Brusic / Tierra K Buck / Haley Varnum / Pan Yang / Linzy M Malcolm / So Yoen Choi / William M de Souza / Isaac M Chiu / Hisashi Umemori / Scott C Weaver / Kenneth S Plante / Jonathan Abraham /
Abstract: Western equine encephalitis virus (WEEV) is an arbovirus that historically caused large outbreaks of encephalitis throughout the Americas. WEEV binds protocadherin 10 (PCDH10) as a receptor, and ...Western equine encephalitis virus (WEEV) is an arbovirus that historically caused large outbreaks of encephalitis throughout the Americas. WEEV binds protocadherin 10 (PCDH10) as a receptor, and highly virulent ancestral WEEV strains also bind low-density lipoprotein receptor (LDLR)-related proteins. As WEEV declined as a human pathogen in North America over the past century, isolates have lost the ability to bind mammalian receptors while still recognizing avian receptors. To explain shifts in receptor dependencies and assess the risk of WEEV re-emergence, we determined cryoelectron microscopy structures of WEEV bound to human PCDH10, avian PCDH10, and human very-low-density lipoprotein receptor (VLDLR). We show that one to three E2 glycoprotein substitutions are sufficient for a nonpathogenic strain to regain the ability to bind mammalian receptors. A soluble VLDLR fragment protects mice from lethal challenge by a virulent ancestral WEEV strain. Because WEEV recently re-emerged in South America after decades of inactivity, our findings have important implications for outbreak preparedness.
History
DepositionSep 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2026Group: Data collection / Database references
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike glycoprotein E1
B: Structural polyprotein
C: Spike glycoprotein E1
D: Structural polyprotein
E: Spike glycoprotein E1
F: Structural polyprotein
G: Cadherin domain-containing protein
H: Cadherin domain-containing protein
I: Cadherin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,80721
Polymers310,1539
Non-polymers2,65412
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 Spike glycoprotein E1 / E1 envelope glycoprotein


Mass: 46717.980 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Western equine encephalitis virus / Production host: Homo sapiens (human) / References: UniProt: P13897
#2: Protein Structural polyprotein / p130


Mass: 44831.969 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Western equine encephalitis virus / Production host: Homo sapiens (human) / References: UniProt: C7EPF4
#3: Protein Cadherin domain-containing protein


Mass: 11834.219 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Passer domesticus (house sparrow) / Production host: Homo sapiens (human) / References: UniProt: A0A8D2M0X8
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
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

Component
IDNameTypeEntity IDParent-IDSource
1western equine encephalitis virus Imperial 181 VLP in complex with house sparrow PCDH10 EC1COMPLEX#30RECOMBINANT
2western equine encephalitis virus Imperial 181 VLPCOMPLEX#21RECOMBINANT
3Protocadherin 10COMPLEX#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Western equine encephalitis virus11039
32Western equine encephalitis virus11039
43Passer domesticus (house sparrow)48849
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Buffer solutionpH: 7.5
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: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 0.96 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22304 / Symmetry type: POINT
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00322218
ELECTRON MICROSCOPYf_angle_d0.75330257
ELECTRON MICROSCOPYf_dihedral_angle_d4.8312990
ELECTRON MICROSCOPYf_chiral_restr0.0533463
ELECTRON MICROSCOPYf_plane_restr0.0053860

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