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- EMDB-47118: Structure of western equine encephalitis virus Imperial 181 VLP i... -

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Basic information

Entry
Database: EMDB / ID: EMD-47118
TitleStructure of western equine encephalitis virus Imperial 181 VLP in complex with house sparrow PCDH10 EC1
Map data
Sample
  • Complex: western equine encephalitis virus Imperial 181 VLP in complex with house sparrow PCDH10 EC1
    • Complex: western equine encephalitis virus Imperial 181 VLP
      • Protein or peptide: Structural polyprotein
    • Complex: Protocadherin 10
      • Protein or peptide: Cadherin domain-containing protein
  • Protein or peptide: Spike glycoprotein E1
  • 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 adhesion via plasma membrane adhesion molecules / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / 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 ...togavirin / T=4 icosahedral viral capsid / homophilic cell adhesion via plasma membrane adhesion molecules / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / 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 / 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-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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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 Imperial 181 VLP in complex with house sparrow PCDH10 EC1
Authors: Abraham J / Fan X / Li W
History
DepositionSep 24, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47118.png

Downloads & links

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Map

FileDownload / File: emd_47118.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 340 pix.
= 319.6 Å		0.94 Å/pix.
x 340 pix.
= 319.6 Å		0.94 Å/pix.
x 340 pix.
= 319.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.015327764 - 0.043643784
Average (Standard dev.)0.00018203184 (±0.0021812057)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 319.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47118_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_47118_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 Imperial 181 VLP in complex wit...

EntireName: western equine encephalitis virus Imperial 181 VLP in complex with house sparrow PCDH10 EC1
Components
  • Complex: western equine encephalitis virus Imperial 181 VLP in complex with house sparrow PCDH10 EC1
    • Complex: western equine encephalitis virus Imperial 181 VLP
      • Protein or peptide: Structural polyprotein
    • Complex: Protocadherin 10
      • Protein or peptide: Cadherin domain-containing protein
  • Protein or peptide: Spike glycoprotein E1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: western equine encephalitis virus Imperial 181 VLP in complex wit...

SupramoleculeName: western equine encephalitis virus Imperial 181 VLP in complex with house sparrow PCDH10 EC1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3
Source (natural)Organism: Western equine encephalitis virus

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Supramolecule #2: western equine encephalitis virus Imperial 181 VLP

SupramoleculeName: western equine encephalitis virus Imperial 181 VLP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
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: #3
Source (natural)Organism: Passer domesticus (house sparrow)

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Macromolecule #1: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 46.71798 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCK FHTVIPSPQV KCCGSLECKA SSRADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTAHLDTFVN GVTPGSSRDL K VIAGPISA ...String:
FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCK FHTVIPSPQV KCCGSLECKA SSRADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTAHLDTFVN GVTPGSSRDL K VIAGPISA AFSPFDHKVV IRKGFVYNYD FPEYGAMKPG AFGDIQASSL DATDIVARTD IRLLKPSVKN IHVPYTQAVS GY EMWKNNS GRPLQETAPF GCKIEVEPLR ASNCAYGHIP ISIDIPDAAF VRSSESPTIL EVSCTVADCI YSADFGGSLT LQY KADREG HCPVHSHSTT AVLKEATTHV TAVGSITLHF STSSPQANFI VSLCGKKSTC NAECKPPADH IIGEPHKVDQ EFQA AVSTT 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: 3 / Enantiomer: LEVO
Source (natural)Organism: Western equine encephalitis virus
Molecular weightTheoretical: 44.831969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SITDDFTLTS PYLGFCPYCR HSTPCFSPIK IENVWDESDD GSIRIQVSAQ FGYNQAGTAD VTKFRYMSFD HDHDIKEDSM EKIAISTSG PCRRLGHKGY FLLAQCPPGD SVTVSITSGT AENSCTVERK IRRKFVGREE YLLPPIHGKQ VKCHVYDHLK E TSAGYITM ...String:
SITDDFTLTS PYLGFCPYCR HSTPCFSPIK IENVWDESDD GSIRIQVSAQ FGYNQAGTAD VTKFRYMSFD HDHDIKEDSM EKIAISTSG PCRRLGHKGY FLLAQCPPGD SVTVSITSGT AENSCTVERK IRRKFVGREE YLLPPIHGKQ VKCHVYDHLK E TSAGYITM HRPGPHAYKS YLEEASGEVY IKPPSGKNVT YECKCGDYST GIVSTRTKIN GCTKAKQCIA YKSDQTKWVF NS PDLIRHT DHSVQGKLHI PFRLTPTVCP VPLAHTPTVM KWFKGITLHL TATRPTLLTT RKLGLRADAT AEWITGTTSR NFS VGREGL EYVWGNHEPV RVWAQESAPG DPHGWPHEII IHYYHRHPVY TVIVLCGVAL AILVGTASSA ACISKARRDC LTPY A

UniProtKB: Structural polyprotein

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Macromolecule #3: Cadherin domain-containing protein

MacromoleculeName: Cadherin domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Passer domesticus (house sparrow)
Molecular weightTheoretical: 11.834219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QLHYTVQEEQ EHGTFVGNIA EDLGLDITKL SARRFQTAPN SRSPYLELNL ETGVLYVNEK IDREQICKQS PSCLLHLEVF LENPLELFR VEIEVLDIND NPPS

UniProtKB: Cadherin domain-containing protein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 12 / 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: FEI FALCON IV (4k x 4k) / Average electron dose: 0.96 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

5210

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22304
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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