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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 / 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 | ||||||
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: To Be Published Title: Structural basis for VLDLR recognition by eastern equine encephalitis virus Authors: Abraham, J. / Yang, P. / Li, W. / Fan, X. / Pan, J. | ||||||
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 | 826.8 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 | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8ua4_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8ua4_validation.xml.gz | 109.9 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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-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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