[English] 日本語
Yorodumi- EMDB-42050: Structure of eastern equine encephalitis virus VLP in complex wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42050 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of eastern equine encephalitis virus VLP in complex with VLDLR LA1 | |||||||||
Map data | icosahedral asymmetrical unit subparticle map | |||||||||
Sample |
| |||||||||
Keywords | Alphaviruses / Receptor / VIRUS LIKE PARTICLE | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.58 Å | |||||||||
Authors | Abraham J / Yang P / Li W / Fan X / Pan J | |||||||||
Funding support | United States, 1 items
| |||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_42050.map.gz | 47.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-42050-v30.xml emd-42050.xml | 27.6 KB 27.6 KB | Display Display | EMDB header |
Images | emd_42050.png | 59.9 KB | ||
Filedesc metadata | emd-42050.cif.gz | 7 KB | ||
Others | emd_42050_additional_1.map.gz emd_42050_additional_2.map.gz emd_42050_half_map_1.map.gz emd_42050_half_map_2.map.gz | 48.5 MB 47.4 MB 47.4 MB 47.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42050 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42050 | HTTPS FTP |
-Validation report
Summary document | emd_42050_validation.pdf.gz | 795.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_42050_full_validation.pdf.gz | 795.3 KB | Display | |
Data in XML | emd_42050_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | emd_42050_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42050 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42050 | HTTPS FTP |
-Related structure data
Related structure data | 8ua4MC 8ua9C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_42050.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | icosahedral asymmetrical unit subparticle map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: sharpened icosahedral asymmetrical unit subparticle map focused on...
File | emd_42050_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | sharpened icosahedral asymmetrical unit subparticle map focused on VLDLR for alignments | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: sharpened icosahedral asymmetrical unit subparticle map
File | emd_42050_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | sharpened icosahedral asymmetrical unit subparticle map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 2
File | emd_42050_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 1
File | emd_42050_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Eastern equine encephalitis virus
+Supramolecule #1: Eastern equine encephalitis virus
+Supramolecule #2: EEEV strain PE6 mature glycoprotein E1
+Supramolecule #3: EEEV strain PE6 mature glycoprotein E2
+Supramolecule #4: EEEV strain PE6 mature glycoprotein E3
+Supramolecule #5: EEEV strain PE6 mature capsid protein
+Supramolecule #6: VLDLR
+Macromolecule #1: Envelope glycoprotein E1
+Macromolecule #2: Envelope glycoprotein E2
+Macromolecule #3: Capsid protein
+Macromolecule #4: Envelope glycoprotein E3
+Macromolecule #5: Very low-density lipoprotein receptor
+Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #7: CALCIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 185420 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |