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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 / homophilic cell-cell adhesion / nervous system development / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / postsynaptic membrane / cell adhesion / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity ...togavirin / T=4 icosahedral viral capsid / homophilic cell-cell adhesion / nervous system development / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / 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 nucleus / host cell plasma membrane / glutamatergic synapse / virion membrane / 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 / 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: To Be Published
Title: Structure of western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1
Authors: Abraham J / Fan X / Li W
History
DepositionSep 24, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing 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
Brightness
Contrast
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47116_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47116_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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