+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5296 | |||||||||
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Title | cryo-EM reconstruction of West Nile virus | |||||||||
Map data | This is a reconstruction map of West Nile virus | |||||||||
Sample |
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Keywords | West Nile Virus | |||||||||
Function / homology | Function and homology information flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | West Nile virus | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 10.3 Å | |||||||||
Authors | Zhang W / Kaufmann B / Chipman PR / Kuhn RJ / Rossmann MG | |||||||||
Citation | Journal: J Struct Biol / Year: 2013 Title: Membrane curvature in flaviviruses. Authors: Wei Zhang / Bärbel Kaufmann / Paul R Chipman / Richard J Kuhn / Michael G Rossmann / Abstract: Coordinated interplay between membrane proteins and the lipid bilayer is required for such processes as transporter function and the entrance of enveloped viruses into host cells. In this study, ...Coordinated interplay between membrane proteins and the lipid bilayer is required for such processes as transporter function and the entrance of enveloped viruses into host cells. In this study, three-dimensional cryo-electron microscopy density maps of mature and immature flaviviruses were analyzed to assess the curvature of the membrane leaflets and its relation to membrane-bound viral glycoproteins. The overall morphology of the viral membrane is determined by the icosahedral scaffold composed of envelope (E) and membrane (M) proteins through interaction of the proteins' stem-anchor regions with the membrane. In localized regions, small membrane areas exhibit convex, concave, flat or saddle-shaped surfaces that are constrained by the specific protein organization within each membrane leaflet. These results suggest that the organization of membrane proteins in small enveloped viruses mediate the formation of membrane curvature. | |||||||||
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_5296.map.gz | 23.6 MB | EMDB map data format | |
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Header (meta data) | emd-5296-v30.xml emd-5296.xml | 9.6 KB 9.6 KB | Display Display | EMDB header |
Images | emd_5296_1.jpg | 89.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5296 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5296 | HTTPS FTP |
-Validation report
Summary document | emd_5296_validation.pdf.gz | 361 KB | Display | EMDB validaton report |
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Full document | emd_5296_full_validation.pdf.gz | 360.6 KB | Display | |
Data in XML | emd_5296_validation.xml.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5296 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5296 | HTTPS FTP |
-Related structure data
Related structure data | 3j0bMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5296.map.gz / Format: CCP4 / Size: 61.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a reconstruction map of West Nile virus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.95 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 : West Nile Virus
Entire | Name: West Nile Virus |
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Components |
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-Supramolecule #1000: West Nile Virus
Supramolecule | Name: West Nile Virus / type: sample / ID: 1000 / Number unique components: 3 |
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-Supramolecule #1: West Nile virus
Supramolecule | Name: West Nile virus / type: virus / ID: 1 / Name.synonym: West Nile Virus / NCBI-ID: 11082 / Sci species name: West Nile virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: West Nile Virus |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Virus shell | Shell ID: 1 / Name: E / Diameter: 500 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Details: 12 mM Tris-HCl,120 mM NaCl, 1 mM EDTA |
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Staining | Type: NEGATIVE / Details: none |
Grid | Details: 400 mesh holey carbon grid |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER / Details: vitrification carried out in a BSL3 lab |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
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Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 83 / Average electron dose: 30 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 47440 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 0.321 µm / Nominal defocus min: 0.112 µm |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle min: 0 / Tilt angle max: 0 |
-Image processing
CTF correction | Details: each particle |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 10.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3DEM / Number images used: 1556 |