+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2296 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The 14 A Cryo-EM structure of Dengue virus at 37C | |||||||||
Map data | Reconstruction of one particles class in the "breathing" dengue virus particles | |||||||||
Sample |
| |||||||||
Keywords | dengue / breathing structure / dynamic structure | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / channel activity / monoatomic ion transmembrane transport / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / channel activity / monoatomic ion transmembrane transport / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / 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 / viral envelope / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Dengue virus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.7 Å | |||||||||
Authors | Fibriansah G / Ng TS / Kostyuchenko VA / Lee S / Wang J / Lok SM | |||||||||
Citation | Journal: J Virol / Year: 2013 Title: Structural changes in dengue virus when exposed to a temperature of 37°C. Authors: Guntur Fibriansah / Thiam-Seng Ng / Victor A Kostyuchenko / Jaime Lee / Sumarlin Lee / Jiaqi Wang / Shee-Mei Lok / Abstract: Previous binding studies of antibodies that recognized a partially or fully hidden epitope suggest that insect cell-derived dengue virus undergoes structural changes at an elevated temperature. This ...Previous binding studies of antibodies that recognized a partially or fully hidden epitope suggest that insect cell-derived dengue virus undergoes structural changes at an elevated temperature. This was confirmed by our cryo-electron microscopy images of dengue virus incubated at 37°C, where viruses change their surface from smooth to rough. Here we present the cryo-electron microscopy structures of dengue virus at 37°C. Image analysis showed four classes of particles. The three-dimensional (3D) map of one of these classes, representing half of the imaged virus population, shows that the E protein shell has expanded and there is a hole at the 3-fold vertices. Fitting E protein structures into the map suggests that all of the interdimeric and some intradimeric E protein interactions are weakened. The accessibility of some previously found cryptic epitopes on this class of particles is discussed. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
-Downloads & links
-EMDB archive
Map data | emd_2296.map.gz | 155.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-2296-v30.xml emd-2296.xml | 9.6 KB 9.6 KB | Display Display | EMDB header |
Images | emd_2296.png | 259.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2296 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2296 | HTTPS FTP |
-Validation report
Summary document | emd_2296_validation.pdf.gz | 245.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_2296_full_validation.pdf.gz | 244.4 KB | Display | |
Data in XML | emd_2296_validation.xml.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2296 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2296 | HTTPS FTP |
-Related structure data
Related structure data | 3zkoMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_2296.map.gz / Format: CCP4 / Size: 465.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of one particles class in the "breathing" dengue virus particles | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Dengue Virus 2
Entire | Name: Dengue Virus 2 |
---|---|
Components |
|
-Supramolecule #1000: Dengue Virus 2
Supramolecule | Name: Dengue Virus 2 / type: sample / ID: 1000 / Oligomeric state: full dengue virion / Number unique components: 1 |
---|
-Supramolecule #1: Dengue virus 2
Supramolecule | Name: Dengue virus 2 / type: virus / ID: 1 / NCBI-ID: 11060 / Sci species name: Dengue virus 2 / Sci species strain: New Guinea C / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
---|---|
Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Host system | Organism: Aedes albopictus (Asian tiger mosquito) / Recombinant cell: C6/36 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Details: 10 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA |
---|---|
Grid | Details: lacey carbon grid, layered with ultra thin carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV Method: 2.5 microlitres virus sample was added per grid and blotted with filter paper for 2.5 s before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Temperature | Average: 100 K |
Date | Nov 21, 2011 |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN / Number real images: 302 / Average electron dose: 18.5 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected manually |
---|---|
CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, EMAN2, MPSA / Details: The particles were selected manually. / Number images used: 5861 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C |
---|---|
Software | Name: Chimera |
Details | Individual envelope protein molecules were fitted separately by manual docking using program O |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation |
Output model | PDB-3zko: |