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Yorodumi- EMDB-2141: 6A Electron cryomicroscopy structure of immature Dengue virus ser... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2141 | |||||||||
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Title | 6A Electron cryomicroscopy structure of immature Dengue virus serotype 1 | |||||||||
Map data | immature Dengue virus 1 | |||||||||
Sample |
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Keywords | flavivirus / dengue virus serotype 1 / immature / e protein / prM protein / capsid protein | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / ribonucleoside triphosphate phosphatase activity / channel activity / double-stranded RNA binding / viral capsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / ribonucleoside triphosphate phosphatase activity / channel activity / double-stranded RNA binding / viral capsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / 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 / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Dengue virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.0 Å | |||||||||
Authors | Kostyuchenko VA / Zhang Q / Tan LC / Ng TS / Lok SM | |||||||||
Citation | Journal: J Virol / Year: 2013 Title: Immature and mature dengue serotype 1 virus structures provide insight into the maturation process. Authors: Victor A Kostyuchenko / Qian Zhang / Joanne L Tan / Thiam-Seng Ng / Shee-Mei Lok / Abstract: Dengue virus is a major human pathogen that has four serotypes (DENV1 to -4). Here we report the cryoelectron microscopy (cryo-EM) structures of immature and mature DENV1 at 6- and 4.5-Å resolution, ...Dengue virus is a major human pathogen that has four serotypes (DENV1 to -4). Here we report the cryoelectron microscopy (cryo-EM) structures of immature and mature DENV1 at 6- and 4.5-Å resolution, respectively. The subnanometer-resolution maps allow accurate placement of all of the surface proteins. Although the immature and mature viruses showed vastly different surface protein organizations, the envelope protein transmembrane (E-TM) regions remain in similar positions. The pivotal role of the E-TM regions leads to the identification of the start and end positions of all surface proteins during maturation. | |||||||||
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_2141.map.gz | 253.7 MB | EMDB map data format | |
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Header (meta data) | emd-2141-v30.xml emd-2141.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | emd_2141.png | 434.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2141 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2141 | HTTPS FTP |
-Validation report
Summary document | emd_2141_validation.pdf.gz | 322.1 KB | Display | EMDB validaton report |
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Full document | emd_2141_full_validation.pdf.gz | 321.3 KB | Display | |
Data in XML | emd_2141_validation.xml.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2141 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2141 | HTTPS FTP |
-Related structure data
Related structure data | 4b03MC 2142C 4cctC 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_2141.map.gz / Format: CCP4 / Size: 804.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | immature Dengue virus 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 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 virus serotype 1
Entire | Name: Immature Dengue virus serotype 1 |
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Components |
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-Supramolecule #1000: Immature Dengue virus serotype 1
Supramolecule | Name: Immature Dengue virus serotype 1 / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 14.5 MDa / Theoretical: 14.5 MDa Method: estimation based on components' amino acid sequences |
-Supramolecule #1: Dengue virus 1
Supramolecule | Name: Dengue virus 1 / type: virus / ID: 1 / NCBI-ID: 11053 / Sci species name: Dengue virus 1 / Sci species strain: PVP159 (DEN1/SG/07K3640DK1/2008) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Aedes aegypti (yellow fever mosquito) / synonym: INVERTEBRATES |
Molecular weight | Experimental: 14.5 MDa / Theoretical: 14.5 MDa |
Virus shell | Shell ID: 1 / Name: E / Diameter: 600 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Details: thin carbon film on lacey carbon support, copper grid, plasma cleaned and glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV / Method: blot 1 second before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 99 K / Max: 101 K / Average: 100 K |
Alignment procedure | Legacy - Astigmatism: Astigmatism was corrected at 250,000 magnification |
Specialist optics | Energy filter - Name: FEI |
Date | Apr 11, 2012 |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Number real images: 838 / Average electron dose: 17.7 e/Å2 / Details: CCD data / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | particles were manually selected |
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CTF correction | Details: Wiener filter weighting each particle during 3D reconstruction |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: GPU-adapted, EMAN1 / Number images used: 7169 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: C |
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Software | Name: Chimera |
Details | Protocol: rigid body. Fit in map feature in Chimera, whole structure was fitted as a rigid body with no apparent need to fit domains separately |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4b03: |