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Yorodumi- PDB-8ua4: Structure of eastern equine encephalitis virus VLP in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ua4 | ||||||
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Title | Structure of eastern equine encephalitis virus VLP in complex with VLDLR LA1 | ||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / Alphaviruses / Receptor | ||||||
Function / homology | Function and homology information reelin receptor activity / VLDL clearance / glycoprotein transport / very-low-density lipoprotein particle binding / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / Reelin signalling pathway / reelin-mediated signaling pathway / low-density lipoprotein particle receptor activity / togavirin ...reelin receptor activity / VLDL clearance / glycoprotein transport / very-low-density lipoprotein particle binding / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / Reelin signalling pathway / reelin-mediated signaling pathway / low-density lipoprotein particle receptor activity / togavirin / very-low-density lipoprotein particle clearance / very-low-density lipoprotein particle / T=4 icosahedral viral capsid / positive regulation of dendrite development / 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 / cytoplasm Similarity search - Function | ||||||
Biological species | Eastern equine encephalitis virus Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 Å | ||||||
Authors | Abraham, J. / Yang, P. / Li, W. / Fan, X. / Pan, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ua4.cif.gz | 828.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ua4.ent.gz | 671.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ua4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ua4_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8ua4_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8ua4_validation.xml.gz | 109.8 KB | Display | |
Data in CIF | 8ua4_validation.cif.gz | 174.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/8ua4 ftp://data.pdbj.org/pub/pdb/validation_reports/ua/8ua4 | HTTPS FTP |
-Related structure data
Related structure data | 42050MC 8ua9C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Envelope glycoprotein ... , 3 types, 12 molecules ADGJBEHKMNOP
#1: Protein | Mass: 47984.246 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Eastern equine encephalitis virus strain PE6 mature envelope glycoprotein E1 Source: (gene. exp.) Eastern equine encephalitis virus / Strain: PE6 / Gene: E1 / Cell line (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: Q88678 #2: Protein | Mass: 47047.020 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Eastern equine encephalitis virus strain PE6 mature envelope glycoprotein E2 Source: (gene. exp.) Eastern equine encephalitis virus / Strain: PE6 / Gene: E2 / Cell line (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: Q88678, togavirin #4: Protein | Mass: 7219.331 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eastern equine encephalitis virus / Strain: PE6 / Cell line (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: P08768 |
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-Protein / Protein/peptide / Sugars / Non-polymers , 4 types, 18 molecules CFILR
#3: Protein | Mass: 29178.846 Da / Num. of mol.: 4 / Mutation: K67N Source method: isolated from a genetically manipulated source Details: Eastern equine encephalitis virus mature capsid protein K67N mutant Source: (gene. exp.) Eastern equine encephalitis virus / Strain: PE6 / Cell line (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: Q88678 #5: Protein/peptide | | Mass: 4015.421 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: human very low-density lipoprotein receptor (VLDLR) LA1 Source: (gene. exp.) Homo sapiens (human) / Gene: VLDLR / Cell line (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: P98155 #6: Sugar | ChemComp-NAG / #7: Chemical | ChemComp-CA / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | |||||||||||||||||||||||||||||||||||||||||||||||||
Natural host |
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Buffer solution | pH: 7.2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 53 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185420 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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