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- EMDB-62802: Structure of WEEV strain 71V1658 virus-like particles (VLPs) in c... -

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Basic information

Entry
Database: EMDB / ID: EMD-62802
TitleStructure of WEEV strain 71V1658 virus-like particles (VLPs) in complex with human PCDH10 extracellular cadherin repeats 1-2 (EC1-EC2)(3-fold region)
Map data
Sample
  • Virus: Western equine encephalitis virus
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Protocadherin-10
KeywordsWEEV / VLP / E2-E1 glycoproteins / receptor / VIRAL PROTEIN
Function / homology
Function and homology information


T=4 icosahedral viral capsid / homophilic cell adhesion via plasma membrane adhesion molecules / nervous system development / postsynaptic membrane / host cell cytoplasm / cell adhesion / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / calcium ion binding / symbiont entry into host cell ...T=4 icosahedral viral capsid / homophilic cell adhesion via plasma membrane adhesion molecules / nervous system development / postsynaptic membrane / host cell cytoplasm / cell adhesion / 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 / glutamatergic synapse / virion membrane / structural molecule activity / proteolysis / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsLiang S / Yang Y / Liu Y / Rao Z / Wang Y / Lou Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for engagement of Western Equine Encephalitis Virus with the PCDH10 receptor.
Authors: Shengjian Liang / Yan Yang / Yixiao Liu / Zhili Xu / Jichao Hou / Donghan Li / Lixin Zhao / Chuyu Hu / Xiaoke Liu / Zihe Rao / Yanyi Wang / Zhiyong Lou /
Abstract: PCDH10 is a newly identified general receptor for Western equine encephalitis virus (WEEV) members, a group of encephalitic alphaviruses that cause severe diseases in humans and equids. While WEEV ...PCDH10 is a newly identified general receptor for Western equine encephalitis virus (WEEV) members, a group of encephalitic alphaviruses that cause severe diseases in humans and equids. While WEEV typically binds PCDH10 as a receptor, nonpathogenic strains have evolved to lose mammalian PCDH10 binding, retaining only avian PCDH10 affinity. Virulent strains also engage VLDLR and ApoER2 as alternative receptors. Here, we determine the structure of WEEV strain 71V1658 virus-like particles (VLPs) in complex with human PCDH10 extracellular cadherin repeats 1-2 (EC1-EC2) by cryo-electron microscopy at 2.99 Å resolution. EC1 inserts into a cleft clamped by two adjacent E2-E1 heterodimers within a single trimeric spike, whereas EC2 maintains no contact with the WEEV VLP. Mutagenesis studies elucidate the impacts of the interacting residues on PCDH10. And residue 153 of E2 is crucial for PCDH10 binding, and the Q153L mutation observes in the nonpathogenic strain Imperial-181 restores its ability to bind to PCDH10. Moreover, the arginine residue at position 89 on avian PCDH10 is essential for its interaction with strain Imperial-181. These results advance our understanding of receptor recognition by alphaviruses and the shift in receptor usage, providing insights for the development of antiviral therapies.
History
DepositionDec 19, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBc / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_62802.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 5.49
Minimum - Maximum-0.51632744 - 19.641425999999999
Average (Standard dev.)0.08730182 (±0.8450618)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Western equine encephalitis virus

EntireName: Western equine encephalitis virus
Components
  • Virus: Western equine encephalitis virus
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Protocadherin-10

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Supramolecule #1: Western equine encephalitis virus

SupramoleculeName: Western equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11039 / Sci species name: Western equine encephalitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 47.326781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCK FHTVIPSPQV KCCGSLECKA SSKADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTAHLDTFVN GVTPGSSRDL K VIAGPISA ...String:
FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCK FHTVIPSPQV KCCGSLECKA SSKADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTAHLDTFVN GVTPGSSRDL K VIAGPISA AFSPFDHKVV IRKGLVYNYD FPEYGAMKPG AFGDIQASSL DATDIVARTD IRLLKPSVKN IHVPYTQAVS GY EMWKNNS GRPLQETAPF GCKIEVEPLR ASNCAYGHIP ISIDIPDAAF VRSSESPTIL EVSCTVADCI YSADFGGSLT LQY KADREG HCPVHSHSTT AVLKEATTHV TAVGSITLHF STSSPQANFI VSLCGKKSTC NAECKPPADH IIGEPHKVDQ EFQA AVSKT SWNWLLALFG GASSLIVVGL IVLVCSSMLI NTRR

UniProtKB: Structural polyprotein

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Macromolecule #2: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 46.434973 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SITDDFTLTS PYLGFCPYCR HSTPCFSPIK IENVWDESDD GSIRIQVSAQ FGYNQAGTAD VTKFRYMSFD HDHDIKEDSM EKIAISTSG PCRRLGHKGY FLLAQCPPGD SVTVSITSGA SENSCTVEKK IRRKFVGREE YLFPPVHGKL VKCHVYDHLK E TSAGYITM ...String:
SITDDFTLTS PYLGFCPYCR HSTPCFSPIK IENVWDESDD GSIRIQVSAQ FGYNQAGTAD VTKFRYMSFD HDHDIKEDSM EKIAISTSG PCRRLGHKGY FLLAQCPPGD SVTVSITSGA SENSCTVEKK IRRKFVGREE YLFPPVHGKL VKCHVYDHLK E TSAGYITM HRPGPHAYKS YLEEASGEVY IKPPSGKNVT YECKCGDYST GIVSTRTKMN GCTKAKQCIA YKSDQTKWVF NS PDLIRHT DHSVQGKLHI PFRLTPTVCP VPLAHTPTVT KWFKGITLHL TAMRPTLLTT RKLGLRADAT AEWITGSTSR NFS VGREGL EYVWGNHEPV RVWAQESAPG DPHGWPHEII IHYYHRHPVY TVIVLCGVAL AILVGTASSA ACIAKARRDC LTPY ALAPN ATVPTALAVL CCI

UniProtKB: Structural polyprotein

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Macromolecule #3: Protocadherin-10

MacromoleculeName: Protocadherin-10 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.98128 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QLHYTVQEEQ EHGTFVGNIA EDLGLDITKL SARGFQTVPN SRTPYLDLNL ETGVLYVNEK IDREQICKQS PSCVLHLEVF LENPLELFQ VEIEVLD

UniProtKB: Protocadherin-10

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

27389

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 378489
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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