+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5422 | |||||||||
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Title | cryo-EM reconstruction of immature dengue virus | |||||||||
Map data | Reconstruction of immature dengue viral particles | |||||||||
Sample |
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Keywords | immature dengue flavivirus cryo-EM | |||||||||
Function / homology | Function and homology information flavivirin / serine-type peptidase activity / nucleoside-triphosphate phosphatase / double-stranded RNA binding / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / RNA helicase ...flavivirin / serine-type peptidase activity / nucleoside-triphosphate phosphatase / double-stranded RNA binding / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / RNA helicase / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Dengue virus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.5 Å | |||||||||
Authors | Zhang Y / Zhang W / Ogata S / Clements D / Strauss JH / Baker TS / Kuhn RJ / Rossmann MG | |||||||||
Citation | Journal: Structure / Year: 2004 Title: Conformational changes of the flavivirus E glycoprotein. Authors: Ying Zhang / Wei Zhang / Steven Ogata / David Clements / James H Strauss / Timothy S Baker / Richard J Kuhn / Michael G Rossmann / Abstract: Dengue virus, a member of the Flaviviridae family, has a surface composed of 180 copies each of the envelope (E) glycoprotein and the membrane (M) protein. The crystal structure of an N-terminal ...Dengue virus, a member of the Flaviviridae family, has a surface composed of 180 copies each of the envelope (E) glycoprotein and the membrane (M) protein. The crystal structure of an N-terminal fragment of E has been determined and compared with a previously described structure. The primary difference between these structures is a 10 degrees rotation about a hinge relating the fusion domain DII to domains DI and DIII. These two rigid body components were used for independent fitting of E into the cryo-electron microscopy maps of both immature and mature dengue viruses. The fitted E structures in these two particles showed a difference of 27 degrees between the two components. Comparison of the E structure in its postfusion state with that in the immature and mature virions shows a rotation approximately around the same hinge. Flexibility of E is apparently a functional requirement for assembly and infection of flaviviruses. | |||||||||
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_5422.map.gz | 8.8 MB | EMDB map data format | |
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Header (meta data) | emd-5422-v30.xml emd-5422.xml | 7.9 KB 7.9 KB | Display Display | EMDB header |
Images | emd_5422_1.jpg | 135.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5422 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5422 | HTTPS FTP |
-Related structure data
Related structure data | 1tgeMC 1tg8C 1thdC 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_5422.map.gz / Format: CCP4 / Size: 51 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of immature dengue viral particles | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.12 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 : immature dengue particle
Entire | Name: immature dengue particle |
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Components |
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-Supramolecule #1000: immature dengue particle
Supramolecule | Name: immature dengue particle / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 3 |
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-Supramolecule #1: Dengue virus 2
Supramolecule | Name: Dengue virus 2 / type: virus / ID: 1 / Details: Dengue virus 2 strain PR159-S1 / NCBI-ID: 11060 / Sci species name: Dengue virus 2 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Aedes albopictus (Asian tiger mosquito) / synonym: INVERTEBRATES |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: Purdue-manufactured, gravity-driven device. Vitrification carried out in hood. |
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-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Date | Feb 1, 2003 |
Image recording | Digitization - Scanner: ZEISS SCAI |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 4099 |
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