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- EMDB-2141: 6A Electron cryomicroscopy structure of immature Dengue virus ser... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2141 | |||||||||
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Title | 6A Electron cryomicroscopy structure of immature Dengue virus serotype 1 | |||||||||
![]() | immature Dengue virus 1 | |||||||||
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![]() | flavivirus / dengue virus serotype 1 / immature / e protein / prM protein / capsid protein | |||||||||
Function / homology | ![]() 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 / double-stranded RNA binding / viral capsid / protein complex oligomerization / monoatomic ion channel activity / 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 / double-stranded RNA binding / viral capsid / protein complex oligomerization / monoatomic ion channel activity / 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 endoplasmic reticulum membrane / protein dimerization activity / 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 / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.0 Å | |||||||||
![]() | Kostyuchenko VA / Zhang Q / Tan LC / Ng TS / Lok SM | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 253.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.6 KB 10.6 KB | Display Display | ![]() |
Images | ![]() | 434.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 322.1 KB | Display | ![]() |
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Full document | ![]() | 321.3 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4b03MC ![]() 2142C ![]() 4cctC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | immature Dengue virus 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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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: ![]() ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |
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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: ![]() |
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: |