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Yorodumi- EMDB-5210: The structure of the recombinant alphavirus, Western equine encep... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5210 | |||||||||
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Title | The structure of the recombinant alphavirus, Western equine encephalitis virus, revealed by cryoelectron microscopy | |||||||||
Map data | This is a 3D map of Western equine encephalitis virus | |||||||||
Sample |
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Keywords | alphavirus / cryoEM / structure / 3D reconstruction | |||||||||
Biological species | Western equine encephalomyelitis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.0 Å | |||||||||
Authors | Sherman MB / Weaver SC | |||||||||
Citation | Journal: J Virol / Year: 2010 Title: Structure of the recombinant alphavirus Western equine encephalitis virus revealed by cryoelectron microscopy. Authors: Michael B Sherman / Scott C Weaver / Abstract: Western equine encephalitis virus (WEEV; Togaviridae, Alphavirus) is an enveloped RNA virus that is typically transmitted to vertebrate hosts by infected mosquitoes. WEEV is an important cause of ...Western equine encephalitis virus (WEEV; Togaviridae, Alphavirus) is an enveloped RNA virus that is typically transmitted to vertebrate hosts by infected mosquitoes. WEEV is an important cause of viral encephalitis in humans and horses in the Americas, and infection results in a range of disease, from mild flu-like illnesses to encephalitis, coma, and death. In addition to spreading via mosquito vectors, human WEEV infections can potentially occur directly via aerosol transmission. Due to its aerosol infectivity and virulence, WEEV is thus classified as a biological safety level 3 (BSL-3) agent. Because of its highly infectious nature and containment requirements, it has not been possible to investigate WEEV's structure or assembly mechanism using standard structural biology techniques. Thus, to image WEEV and other BSL-3 agents, we have constructed a first-of-its-kind BSL-3 cryoelectron microscopy (cryoEM) containment facility. cryoEM images of WEEV were used to determine the first three-dimensional structure of this important human pathogen. The overall organization of WEEV is similar to those of other alphaviruses, consistent with the high sequence similarity among alphavirus structural proteins. Surprisingly, the nucleocapsid of WEEV, a New World virus, is more similar to the Old World alphavirus Sindbis virus than to other New World alphaviruses. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5210.map.gz | 71.2 MB | EMDB map data format | |
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Header (meta data) | emd-5210-v30.xml emd-5210.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_5210_1.jpg | 112.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5210 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5210 | HTTPS FTP |
-Validation report
Summary document | emd_5210_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
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Full document | emd_5210_full_validation.pdf.gz | 77.2 KB | Display | |
Data in XML | emd_5210_validation.xml.gz | 492 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5210 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5210 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5210.map.gz / Format: CCP4 / Size: 175.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a 3D map of Western equine encephalitis virus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Western equine encephalitis virus
Entire | Name: Western equine encephalitis virus |
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Components |
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-Supramolecule #1000: Western equine encephalitis virus
Supramolecule | Name: Western equine encephalitis virus / type: sample / ID: 1000 Oligomeric state: 80 trimers of E1-E2 glycoproteins, 240 copies of capsid protein, vRNA Number unique components: 4 |
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-Supramolecule #1: Western equine encephalomyelitis virus
Supramolecule | Name: Western equine encephalomyelitis virus / type: virus / ID: 1 / Name.synonym: WEEV / NCBI-ID: 11039 / Sci species name: Western equine encephalomyelitis virus / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No / Syn species name: WEEV |
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Host (natural) | Organism: Equus caballus (horse) / synonym: VERTEBRATES |
Molecular weight | Experimental: 52 MDa / Theoretical: 52 MDa |
Virus shell | Shell ID: 1 / T number (triangulation number): 4 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation #1
Preparation ID | 1 |
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Buffer | pH: 7.4 Details: TEN buffer: 0.05 M Tris-HCl, pH 7.4, 0.1 M NaCl, 0.001 M EDTA |
Grid | Details: R2/2 Quantifoil grids, C-flat grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 80 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger / Method: Blot for 2s |
-Sample preparation #2
Preparation ID | 2 |
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Buffer | pH: 7.4 Details: TEN buffer: 0.05 M Tris-HCl, pH 7.4, 0.1 M NaCl, 0.001 M EDTA |
Grid | Details: R2/2 Quantifoil grids, C-flat grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 80 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger / Method: Blot for 2s |
-Electron microscopy
Microscope | JEOL 2200FS |
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Temperature | Min: 89 K / Max: 95 K / Average: 90 K |
Alignment procedure | Legacy - Astigmatism: 300,000x magnification / Legacy - Electron beam tilt params: 0 |
Specialist optics | Energy filter - Name: omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Nov 15, 2007 |
Image recording | Category: FILM / Film or detector model: GENERIC CCD / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 2.1 µm / Number real images: 49 / Average electron dose: 20 e/Å2 / Od range: 0.9 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 51200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.85 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Eucentric, side entry Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PIF / Number images used: 4586 |