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- EMDB-47116: Structure of western equine encephalitis virus CBA87 VLP in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-47116
TitleStructure of western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1
Map data
Sample
  • Complex: western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1
    • Complex: western equine encephalitis virus CBA87 VLP
      • Protein or peptide: Capsid protein
    • Complex: Protocadherin 10
      • Protein or peptide: Protocadherin-10
  • Protein or peptide: Structural polyprotein
  • Protein or peptide: Structural polyprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordswestern equine encephalitis virus / WEEV / receptor binding / PCDH10 / virus like particles / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / host cell endoplasmic reticulum / homophilic cell-cell adhesion / cell adhesion molecule binding / nervous system development / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm ...togavirin / T=4 icosahedral viral capsid / host cell endoplasmic reticulum / homophilic cell-cell adhesion / cell adhesion molecule binding / nervous system development / 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 / postsynaptic membrane / cell adhesion / 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 / glutamatergic synapse / 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. / Cadherin repeats. / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin ...Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / : / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / 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 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 / Structural polyprotein / Protocadherin-10
Similarity search - Component
Biological speciesWestern equine encephalitis virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsAbraham J / Fan X / Li W
Funding support United States, 2 items
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, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47116.png

Downloads & links

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Map

FileDownload / File: emd_47116.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 312 pix.
= 330.72 Å		1.06 Å/pix.
x 312 pix.
= 330.72 Å		1.06 Å/pix.
x 312 pix.
= 330.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.003787273 - 1.8786256
Average (Standard dev.)0.010807051 (±0.07015676)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 330.71997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_47116_additional_1.map
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Half map: #2

Fileemd_47116_half_map_1.map
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Half map: #1

Fileemd_47116_half_map_2.map
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Sample components

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Entire : western equine encephalitis virus CBA87 VLP in complex with human...

EntireName: western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1
Components
  • Complex: western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1
    • Complex: western equine encephalitis virus CBA87 VLP
      • Protein or peptide: Capsid protein
    • Complex: Protocadherin 10
      • Protein or peptide: Protocadherin-10
  • Protein or peptide: Structural polyprotein
  • Protein or peptide: Structural polyprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: western equine encephalitis virus CBA87 VLP in complex with human...

SupramoleculeName: western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#4
Source (natural)Organism: Western equine encephalitis virus

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Supramolecule #2: western equine encephalitis virus CBA87 VLP

SupramoleculeName: western equine encephalitis virus CBA87 VLP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Western equine encephalitis virus

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Supramolecule #3: Protocadherin 10

SupramoleculeName: Protocadherin 10 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 46.703004 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCK FHTVVPSPQV KCCGSLECKA SSKADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTARLDTFVN GVTPGSSRDL K VIAGPISA ...String:
FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCK FHTVVPSPQV KCCGSLECKA SSKADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTARLDTFVN GVTPGSSRDL K VIAGPISA AFSPFDHKVV IRKGLVYNYD FPEYGAMNPG AFGDIQASSL DATDIVARTD IRLLKPSVKN IHVPYTQAVS GY EMWKNNS GRPLQETAPF GCKIEVEPLR ATNCAYGHIP ISIDIPDAAF VRSSESPTIL EVSCTVADCI YSADFGGSLT LQY KANREG HCPVHSHSTT AVLKEATTHV TATGSITLHF STSSPQANFI VSLCGKKTTC NAECKPPADH IIGEPHKVDQ EFQA AVSKT SWNWLLALFG GASSLIVVGL IVLVCSSML

UniProtKB: Structural polyprotein

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Macromolecule #2: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 45.007211 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SITDDFTLTS PYLGFCPYCR HSAPCFSPIK IENVWDESDD GSIRIQVSAQ FGYNQAGTAD VTKFRYMSYD HDHDIKEDSM EKLAISTSG PCRRLGHKGY FLLAQCPPGD SVTVSITSGA SENSCTVEKK IRRKFVGREE YLFPPVHGKL VKCHVYDHLK E TSAGYITM ...String:
SITDDFTLTS PYLGFCPYCR HSAPCFSPIK IENVWDESDD GSIRIQVSAQ FGYNQAGTAD VTKFRYMSYD HDHDIKEDSM EKLAISTSG PCRRLGHKGY FLLAQCPPGD SVTVSITSGA SENSCTVEKK IRRKFVGREE YLFPPVHGKL VKCHVYDHLK E TSAGYITM HRPGPHAYKS YLEEASGEVY IKPPSGKNVT YECKCGDYST GIVSTRTKMN GCTKAKQCIA YKRDQTKWVF NS PDLIRHT DHSVQGKLHI PFRLTPTVCP VPLAHTPTVT KWFKGITLHL TATRPTLLTT RKLGLRADAT AEWITGTTSR NFS VGREGL EYVWGNHEPV RVWAQESAPG DPHGWPHEII IHYYHRHPVY TVIVLCGVAL AILVGTASSA ACIAKARRDC LTPY ALA

UniProtKB: Structural polyprotein

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Macromolecule #3: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 17.949436 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GKRQRMCMKL ESDKTFPIML NGQVNGYACV VGGRLMKPLH VEGKIDNEQL AAVKLKKASM YDLEYGDVPQ NMKSDTLQYT SDKPPGFYN WHHGAVQYEN GRFTVPRGVG GKGDSGRPIL DNRGRVVAIV LGGANEGTRT ALSVVTWNQK GVTIKDTPEG S EPW

UniProtKB: Structural polyprotein

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Macromolecule #4: Protocadherin-10

MacromoleculeName: Protocadherin-10 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.719038 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QLHYTVQEEQ EHGTFVGNIA EDLGLDITKL SARGFQTVPN SRTPYLDLNL ETGVLYVNEK IDREQICKQS PSCVLHLEVF LENPLELFQ VEIEVLDIND NPPS

UniProtKB: Protocadherin-10

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 16 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.05 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 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:

5210

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13141
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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