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Yorodumi- PDB-8ufc: Eastern equine encephalitis virus (PE-6) VLP in complex with VLDL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ufc | ||||||
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Title | Eastern equine encephalitis virus (PE-6) VLP in complex with VLDLR LA(1-2) (asymmetric unit) | ||||||
Components |
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Keywords | VIRAL PROTEIN / virus / receptor / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID | ||||||
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 / very-low-density lipoprotein particle clearance ...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 / 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 / calcium-dependent protein binding / nervous system development / 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 / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / signal transduction / proteolysis / 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: 3.09 Å | ||||||
Authors | Adams, L.J. / Fremont, D.H. / Center for Structural Biology of Infectious Diseases (CSBID) | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ufc.cif.gz | 722.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ufc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ufc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ufc_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8ufc_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8ufc_validation.xml.gz | 112 KB | Display | |
Data in CIF | 8ufc_validation.cif.gz | 174 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/8ufc ftp://data.pdbj.org/pub/pdb/validation_reports/uf/8ufc | HTTPS FTP |
-Related structure data
Related structure data | 42192MC 8ufaC 8ufbC 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
-Protein , 4 types, 16 molecules ADGJBEHKCFILVWXY
#1: Protein | Mass: 47935.180 Da / Num. of mol.: 4 / Fragment: UNP residues 802-1242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eastern equine encephalitis virus / Strain: PE-6 / Production host: Homo sapiens (human) / References: UniProt: Q88678 #2: Protein | Mass: 46378.191 Da / Num. of mol.: 4 / Fragment: UNP residues 325-738 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eastern equine encephalitis virus / Strain: PE-6 / Production host: Homo sapiens (human) / References: UniProt: Q88678 #3: Protein | Mass: 16540.656 Da / Num. of mol.: 4 / Fragment: UNP residues 111-261 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eastern equine encephalitis virus / Gene: SP / Production host: Homo sapiens (human) / References: UniProt: W8S146 #4: Protein | Mass: 8585.350 Da / Num. of mol.: 4 / Fragment: UNP residues 31-108 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VLDLR / Production host: Homo sapiens (human) / References: UniProt: P98155 |
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-Sugars / Non-polymers , 2 types, 16 molecules
#5: Sugar | ChemComp-NAG / #6: Chemical | ChemComp-CA / |
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-Details
Has ligand of interest | N |
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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
Component | Name: Eastern equine encephalitis virus bound to human VLDLR receptor Type: VIRUS / Entity ID: #1-#4 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Eastern equine encephalitis virus / Strain: PE-6 |
Source (recombinant) | Organism: Homo sapiens (human) |
Details of virus | Empty: YES / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE |
Buffer solution | pH: 7.4 |
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: 2200 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 37.9 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 459518 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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