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- EMDB-38371: Structure of Eastern Equine Encephalitis VLP in complex with the ... -

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Entry
Database: EMDB / ID: EMD-38371
TitleStructure of Eastern Equine Encephalitis VLP in complex with the receptor VLDLR LA3-5
Map data
Sample
  • Complex: East Equine Encephalitis virus VLP in complex with its receptor VLDLR LA3-5 at the asymmetric unit
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Capsid protein
    • Protein or peptide: Very low-density lipoprotein receptor
    • Protein or peptide: Very low-density lipoprotein receptor
  • Ligand: CALCIUM ION
KeywordsEast Equine Encephalitis virus / EEEV / receptor / complex / VLDLR / glycoprotein / VIRAL PROTEIN
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 / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / reelin-mediated signaling pathway ...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 / low-density lipoprotein particle receptor activity / very-low-density lipoprotein particle clearance / reelin-mediated signaling pathway / 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 / cholesterol metabolic process / VLDLR internalisation and degradation / 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 / host cell cytoplasm / receptor complex / symbiont entry into host cell / lysosomal membrane / serine-type endopeptidase activity / 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
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
Very low-density lipoprotein receptor / Structural polyprotein
Similarity search - Component
Biological speciesEastern equine encephalitis virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCao D / Ma B / Cao Z / Xu X / Zhang X / Xiang Y
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
National Natural Science Foundation of China (NSFC) China
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2024
Title: The receptor VLDLR binds Eastern Equine Encephalitis virus through multiple distinct modes.
Authors: Duanfang Cao / Bingting Ma / Ziyi Cao / Xiaoyu Xu / Xinzheng Zhang / Ye Xiang /
Abstract: Eastern Equine Encephalitis virus (EEEV) is an alphavirus that can cause severe diseases in infected humans. The very low-density lipoprotein receptor (VLDLR) was recently identified as a receptor of ...Eastern Equine Encephalitis virus (EEEV) is an alphavirus that can cause severe diseases in infected humans. The very low-density lipoprotein receptor (VLDLR) was recently identified as a receptor of EEEV. Herein, we performed cryo-electron microscopy structural and biochemistry studies on the specific interactions between EEEV and VLDLR. Our results show that VLDLR binds EEEV at three different sites A, B and C through its membrane-distal LDLR class A (LA) repeats. Site A is located in the cleft in between the E1-E2 heterodimers. Site B is located near the connecting β ribbon of E2 and is in proximity to site A, while site C is on the domain B of E2. The binding of VLDLR LAs to EEEV is in complex modes, including the LA1-2 and LA3-5 mediated two major modes. Disruption of the LA1-2 mediated binding significantly affect the cell attachment of EEEV. However, the mutation W132G of VLDLR impairs the binding of LA3, drives the switch of the binding modes, and significantly enhances the attachment of EEEV to the cell. The W132G variant of VLDLR could be identified in human genome and SNP sequences, implying that people with similar mutations in VLDLR may be highly susceptible to EEEV infection.
History
DepositionDec 19, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38371.png

Downloads & links

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Map

FileDownload / File: emd_38371.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 220 pix.
= 292.6 Å		1.33 Å/pix.
x 220 pix.
= 292.6 Å		1.33 Å/pix.
x 220 pix.
= 292.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.0949203 - 0.15670896
Average (Standard dev.)0.0010259569 (±0.008641645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 292.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38371_msk_1.map
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Half map: #2

Fileemd_38371_half_map_1.map
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Half map: #1

Fileemd_38371_half_map_2.map
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Sample components

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Entire : East Equine Encephalitis virus VLP in complex with its receptor V...

EntireName: East Equine Encephalitis virus VLP in complex with its receptor VLDLR LA3-5 at the asymmetric unit
Components
  • Complex: East Equine Encephalitis virus VLP in complex with its receptor VLDLR LA3-5 at the asymmetric unit
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Capsid protein
    • Protein or peptide: Very low-density lipoprotein receptor
    • Protein or peptide: Very low-density lipoprotein receptor
  • Ligand: CALCIUM ION

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Supramolecule #1: East Equine Encephalitis virus VLP in complex with its receptor V...

SupramoleculeName: East Equine Encephalitis virus VLP in complex with its receptor VLDLR LA3-5 at the asymmetric unit
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Eastern equine encephalitis virus / Strain: strain PE6

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Macromolecule #1: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Eastern equine encephalitis virus
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: Spike glycoprotein E2

MacromoleculeName: Spike glycoprotein E2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Eastern equine encephalitis virus
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: GenBank AAU95735.1 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Eastern equine encephalitis virus
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: Very low-density lipoprotein receptor

MacromoleculeName: Very low-density lipoprotein receptor / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.428696 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PTCGAHEFQC STSSCIPISW VCDDDADCSD QSDESLEQCG R

UniProtKB: Very low-density lipoprotein receptor

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Macromolecule #5: Very low-density lipoprotein receptor

MacromoleculeName: Very low-density lipoprotein receptor / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.532837 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RTCRIHEISC GAHSTQCIPV SWRCDGENDC DSGEDEENCG N

UniProtKB: Very low-density lipoprotein receptor

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 8 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14840
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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