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- EMDB-42050: Structure of eastern equine encephalitis virus VLP in complex wit... -

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Entry
Database: EMDB / ID: EMD-42050
TitleStructure of eastern equine encephalitis virus VLP in complex with VLDLR LA1
Map dataicosahedral asymmetrical unit subparticle map
Sample
  • Virus: Eastern equine encephalitis virus
    • Complex: EEEV strain PE6 mature glycoprotein E1
      • Protein or peptide: Envelope glycoprotein E1
    • Complex: EEEV strain PE6 mature glycoprotein E2
      • Protein or peptide: Envelope glycoprotein E2
    • Complex: EEEV strain PE6 mature glycoprotein E3
      • Protein or peptide: Envelope glycoprotein E3
    • Complex: EEEV strain PE6 mature capsid protein
      • Protein or peptide: Capsid protein
    • Complex: VLDLR
      • Protein or peptide: Very low-density lipoprotein receptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsAlphaviruses / Receptor / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


reelin receptor activity / VLDL clearance / glycoprotein transport / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / Reelin signalling pathway / very-low-density lipoprotein particle binding / reelin-mediated signaling pathway / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance ...reelin receptor activity / VLDL clearance / glycoprotein transport / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / Reelin signalling pathway / very-low-density lipoprotein particle binding / reelin-mediated signaling pathway / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / togavirin / very-low-density lipoprotein particle / positive regulation of dendrite development / T=4 icosahedral viral capsid / dendrite morphogenesis / cargo receptor activity / lipid transport / apolipoprotein binding / clathrin-coated pit / VLDLR internalisation and degradation / cholesterol metabolic process / receptor-mediated endocytosis / memory / symbiont-mediated suppression of host gene expression / calcium-dependent protein binding / nervous system development / symbiont-mediated suppression of host toll-like receptor signaling pathway / receptor complex / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / lysosomal membrane / fusion of virus membrane with host endosome membrane / calcium ion binding / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / signal transduction / proteolysis / RNA binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein ...: / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / 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. / Low-density lipoprotein receptor domain class A / : / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Calcium-binding EGF domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein / Very low-density lipoprotein receptor / Structural polyprotein
Similarity search - Component
Biological speciesEastern equine encephalitis virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsAbraham J / Yang P / Li W / Fan X / Pan J
Funding support United States, 1 items
OrganizationGrant numberCountry
Burroughs Wellcome Fund United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for VLDLR recognition by eastern equine encephalitis virus.
Authors: Pan Yang / Wanyu Li / Xiaoyi Fan / Junhua Pan / Colin J Mann / Haley Varnum / Lars E Clark / Sarah A Clark / Adrian Coscia / Himanish Basu / Katherine Nabel Smith / Vesna Brusic / Jonathan Abraham /
Abstract: Eastern equine encephalitis virus (EEEV) is the most virulent alphavirus that infects humans, and many survivors develop neurological sequelae, including paralysis and intellectual disability. ...Eastern equine encephalitis virus (EEEV) is the most virulent alphavirus that infects humans, and many survivors develop neurological sequelae, including paralysis and intellectual disability. Alphavirus spike proteins comprise trimers of heterodimers of glycoproteins E2 and E1 that mediate binding to cellular receptors and fusion of virus and host cell membranes during entry. We recently identified very-low density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2) as cellular receptors for EEEV and a distantly related alphavirus, Semliki Forest virus (SFV). Here, we use single-particle cryo-electron microscopy (cryo-EM) to determine structures of the EEEV and SFV spike glycoproteins bound to the VLDLR ligand-binding domain and found that EEEV and SFV interact with the same cellular receptor through divergent binding modes. Our studies suggest that the ability of LDLR-related proteins to interact with viral spike proteins through very small footprints with flexible binding modes results in a low evolutionary barrier to the acquisition of LDLR-related proteins as cellular receptors for diverse sets of viruses.
History
DepositionSep 20, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42050.png

Downloads & links

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Map

FileDownload / File: emd_42050.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationicosahedral asymmetrical unit subparticle map
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.029913211 - 0.07464798
Average (Standard dev.)0.00016683177 (±0.0031208522)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened icosahedral asymmetrical unit subparticle map focused on...

Fileemd_42050_additional_1.map
Annotationsharpened icosahedral asymmetrical unit subparticle map focused on VLDLR for alignments
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpened icosahedral asymmetrical unit subparticle map

Fileemd_42050_additional_2.map
Annotationsharpened icosahedral asymmetrical unit subparticle map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_42050_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_42050_half_map_2.map
Annotationhalf map 1
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
    • Complex: EEEV strain PE6 mature glycoprotein E1
      • Protein or peptide: Envelope glycoprotein E1
    • Complex: EEEV strain PE6 mature glycoprotein E2
      • Protein or peptide: Envelope glycoprotein E2
    • Complex: EEEV strain PE6 mature glycoprotein E3
      • Protein or peptide: Envelope glycoprotein E3
    • Complex: EEEV strain PE6 mature capsid protein
      • Protein or peptide: Capsid protein
    • Complex: VLDLR
      • Protein or peptide: Very low-density lipoprotein receptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Eastern equine encephalitis virus

SupramoleculeName: Eastern equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / NCBI-ID: 11021 / Sci species name: Eastern equine encephalitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Supramolecule #2: EEEV strain PE6 mature glycoprotein E1

SupramoleculeName: EEEV strain PE6 mature glycoprotein E1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Eastern equine encephalitis virus

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Supramolecule #3: EEEV strain PE6 mature glycoprotein E2

SupramoleculeName: EEEV strain PE6 mature glycoprotein E2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Eastern equine encephalitis virus

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Supramolecule #4: EEEV strain PE6 mature glycoprotein E3

SupramoleculeName: EEEV strain PE6 mature glycoprotein E3 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Eastern equine encephalitis virus

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Supramolecule #5: EEEV strain PE6 mature capsid protein

SupramoleculeName: EEEV strain PE6 mature capsid protein / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Eastern equine encephalitis virus

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Supramolecule #6: VLDLR

SupramoleculeName: VLDLR / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #5 / Details: EEEV receptor VLDLR
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein E1

MacromoleculeName: Envelope glycoprotein E1 / type: protein_or_peptide / ID: 1
Details: Eastern equine encephalitis virus strain PE6 mature envelope glycoprotein E1
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Eastern equine encephalitis virus / Strain: PE6
Molecular weightTheoretical: 47.984246 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YEHTAVMPNK VGIPYKALVE RPGYAPVHLQ IQLVNTRIIP STNLEYITCK YKTKVPSPVV KCCGATQCTS KPHPDYQCQV FSGVYPFMW GGAYCFCDTE NTQMSEAYVE RSEECSIDHA KAYKVHTGTV QAMVNITYGS VSWRSADVYV NGETPAKIGD A KLIIGPLS ...String:
YEHTAVMPNK VGIPYKALVE RPGYAPVHLQ IQLVNTRIIP STNLEYITCK YKTKVPSPVV KCCGATQCTS KPHPDYQCQV FSGVYPFMW 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 HIVDYPAQHT ESFT SAISA TAWSWIKVLV GGTSAFIVLG LIATAVVALV LFFHRH

UniProtKB: Structural polyprotein

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Macromolecule #2: Envelope glycoprotein E2

MacromoleculeName: Envelope glycoprotein E2 / type: protein_or_peptide / ID: 2
Details: Eastern equine encephalitis virus strain PE6 mature envelope glycoprotein E2
Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Eastern equine encephalitis virus / Strain: PE6
Molecular weightTheoretical: 47.04702 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 PILLALLCCI KPTRA

UniProtKB: Structural polyprotein

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Macromolecule #3: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 3
Details: Eastern equine encephalitis virus mature capsid protein K67N mutant
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Eastern equine encephalitis virus / Strain: PE6
Molecular weightTheoretical: 29.178846 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFPYPTLNYP PMAPINPMAY RDPNPPRRRW RPFRPPLAAQ IEDLRRSIAS LTLKQRAPNP PAGPPANRKK PAPKPKPAQA KKKRPPPPA KKQKRKPKPG KRQRMCMKLE SDKTFPIMLN GQVNGYACVV GGRVFKPLHV EGRIDNEQLA AIKLKKASIY D LEYGDVPQ ...String:
MFPYPTLNYP PMAPINPMAY RDPNPPRRRW RPFRPPLAAQ IEDLRRSIAS LTLKQRAPNP PAGPPANRKK PAPKPKPAQA KKKRPPPPA KKQKRKPKPG KRQRMCMKLE SDKTFPIMLN GQVNGYACVV GGRVFKPLHV EGRIDNEQLA AIKLKKASIY D LEYGDVPQ CMKSDTLQYT SDKPPGFYNW HHGAVQYENN RFTVPRGVGG KGDSGRPILD NKGRVVAIVL GGVNEGSRTA LS VVTWNQK GVTVKDTPEG SEPW

UniProtKB: Structural polyprotein

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Macromolecule #4: Envelope glycoprotein E3

MacromoleculeName: Envelope glycoprotein E3 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Eastern equine encephalitis virus / Strain: PE6
Molecular weightTheoretical: 7.219331 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SLATVMCVLA NITFPCDQPP CMPCCYEKNP HETLTMLEQN YDSRAYDQLL DAAVKCNARR TRR

UniProtKB: Structural polyprotein

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Macromolecule #5: Very low-density lipoprotein receptor

MacromoleculeName: Very low-density lipoprotein receptor / type: protein_or_peptide / ID: 5
Details: human very low-density lipoprotein receptor (VLDLR) LA1
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.015421 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
CEPSQFQCTN GRCITLLWKC DGDEDCVDGS DEKNCV

UniProtKB: Very low-density lipoprotein receptor

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / 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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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.0 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: 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:

22276

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 185420
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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