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- EMDB-42188: Eastern equine encephalitis virus (PE-6) VLP (asymmetric unit) -

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Basic information

Entry
Database: EMDB / ID: EMD-42188
TitleEastern equine encephalitis virus (PE-6) VLP (asymmetric unit)
Map dataEEEV PE-6 VLP focused reconstruction
Sample
  • Virus: Eastern equine encephalitis virus
    • Protein or peptide: E1 protein
    • Protein or peptide: E2 protein
    • Protein or peptide: Capsid protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsvirus / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / VIRAL PROTEIN
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane
Similarity search - Function
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 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. / 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
Similarity search - Component
Biological speciesEastern equine encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsAdams LJ / Fremont DH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell / Year: 2024
Title: Structural and functional basis of VLDLR usage by Eastern equine encephalitis virus.
Authors: Lucas J Adams / Saravanan Raju / Hongming Ma / Theron Gilliland / Douglas S Reed / William B Klimstra / Daved H Fremont / Michael S Diamond /
Abstract: The very-low-density lipoprotein receptor (VLDLR) comprises eight LDLR type A (LA) domains and supports entry of distantly related alphaviruses, including Eastern equine encephalitis virus (EEEV) and ...The very-low-density lipoprotein receptor (VLDLR) comprises eight LDLR type A (LA) domains and supports entry of distantly related alphaviruses, including Eastern equine encephalitis virus (EEEV) and Semliki Forest virus (SFV). Here, by resolving multiple cryo-electron microscopy structures of EEEV-VLDLR complexes and performing mutagenesis and functional studies, we show that EEEV uses multiple sites (E1/E2 cleft and E2 A domain) to engage more than one LA domain simultaneously. However, no single LA domain is necessary or sufficient to support efficient EEEV infection. Whereas all EEEV strains show conservation of two VLDLR-binding sites, the EEEV PE-6 strain and a few other EEE complex members feature a single amino acid substitution that enables binding of LA domains to an additional site on the E2 B domain. These structural and functional analyses informed the design of a minimal VLDLR decoy receptor that neutralizes EEEV infection and protects mice from lethal challenge.
History
DepositionOct 4, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42188.png

Downloads & links

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Map

FileDownload / File: emd_42188.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEEEV PE-6 VLP focused reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 260 pix.
= 281.06 Å		1.08 Å/pix.
x 260 pix.
= 281.06 Å		1.08 Å/pix.
x 260 pix.
= 281.06 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.081 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.8094594 - 2.4870772
Average (Standard dev.)0.0007090422 (±0.0781886)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 281.06 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: EEEV PE-6 VLP focused reconstruction (unsharpened map)

Fileemd_42188_additional_1.map
AnnotationEEEV PE-6 VLP focused reconstruction (unsharpened map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EEEV PE-6 VLP focused reconstruction (half map B)

Fileemd_42188_half_map_1.map
AnnotationEEEV PE-6 VLP focused reconstruction (half map B)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EEEV PE-6 VLP focused reconstruction (half map A)

Fileemd_42188_half_map_2.map
AnnotationEEEV PE-6 VLP focused reconstruction (half map A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Eastern equine encephalitis virus

EntireName: Eastern equine encephalitis virus
Components
  • Virus: Eastern equine encephalitis virus
    • Protein or peptide: E1 protein
    • Protein or peptide: E2 protein
    • Protein or peptide: Capsid protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Eastern equine encephalitis virus

SupramoleculeName: Eastern equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 11021 / Sci species name: Eastern equine encephalitis virus / Sci species strain: PE-6 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes

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Macromolecule #1: E1 protein

MacromoleculeName: E1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Eastern equine encephalitis virus / Strain: PE-6
Molecular weightTheoretical: 47.93518 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YEHTAVMPNK VGIPYKALVE RPGYAPVHLQ IQLVNTRIIP STNLEYITCK YKTKVPSPVV KCCGATQCTS KPHPDYQCQV FSGVYPFMY GGAYCFCDTE NTQMSEAYVE RSEECSIDHA KAYKVHTGTV QAMVNITYGS VSWRSADVYV NGETPAKIGD A KLIIGPLS ...String:
YEHTAVMPNK VGIPYKALVE RPGYAPVHLQ IQLVNTRIIP STNLEYITCK YKTKVPSPVV KCCGATQCTS KPHPDYQCQV FSGVYPFMY GGAYCFCDTE NTQMSEAYVE RSEECSIDHA KAYKVHTGTV QAMVNITYGS VSWRSADVYV NGETPAKIGD A KLIIGPLS SAWSPFDNKV VVYGHEVYNY DFPEYGTGKA GSFGDLQSRT STSNDLYANT NLKLQRPQAG IVHTPFTQVP SG FERWKKD KGAPLNDVAP FGCSIALEPL RAENCAVGSI PISIDIPDAA FTRISETPTV SDLECKITEC TYAFDFGGIA TVA YKSSKA GNCPIHSPSG VAVIKENDVT LAESGSFTFH FSTANIHPAF KLQVCTSAVT CKGDCKPPKD HIVDYAAQHT ESFT SAISA TAWSWIKVLV GGTSAFIVLG LIATAVVALV LFFHRH

UniProtKB: Structural polyprotein

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Macromolecule #2: E2 protein

MacromoleculeName: E2 protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Eastern equine encephalitis virus / Strain: PE-6
Molecular weightTheoretical: 46.378191 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DLDTHFTQYK LARPYIADCP NCGHSRCDSP IAIEEVRGDA HAGVIRIQTS AMFGLKTDGV DLAYMSFMNG KTQKSIKIDN LHVRTSAPC SLVSHHGYYI LAQCPPGDTV TVGFHDGPNR HTCTVAHKVE FRPVGREKYR HPPEHGVELP CNRYTHKRAD Q GHYVEMHQ ...String:
DLDTHFTQYK LARPYIADCP NCGHSRCDSP IAIEEVRGDA HAGVIRIQTS AMFGLKTDGV DLAYMSFMNG KTQKSIKIDN LHVRTSAPC SLVSHHGYYI LAQCPPGDTV TVGFHDGPNR HTCTVAHKVE FRPVGREKYR HPPEHGVELP CNRYTHKRAD Q GHYVEMHQ PGLVADHSLL SIHSAKVKIT VPSGAQVKYY CKCPDVRKGI TSSDHTTTCT DVKQCRAYLI DNKKWVYNSG RL PRGEGDT FKGKLHVPFV PVKAKCIATL APEPLVEHKH RTLILHLHPD HPTLLTTRSL GSDANPTRQW IERPTTVNFT VTG EGLEYT WGNHPPKRVW AQESGEGNPH GWPHEVVVYY YNRYPLTTII GLCTCVAIIM VSCVTSVWLL CRTRNLCITP YKLA PNAQV PILLALLCC

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
Source (natural)Organism: Eastern equine encephalitis virus / Strain: PE-6
Molecular weightTheoretical: 16.540656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DKTFPIMLNG QVNGYACVVG GRVFKPLHVE GRIDNEQLAA IKLKKASIYD LEYGDVPQCM KSDTLQYTSD KPPGFYNWHH GAVQYENNR FTVPRGVGGK GDSGRPILDN KGRVVAIVLG GVNEGSRTAL SVVTWNQKGV TVKDTPEGSE PW

UniProtKB: Structural polyprotein

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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: 8 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 37.93 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1038056
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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