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Yorodumi- PDB-4cbf: Near-atomic resolution cryo-EM structure of Dengue serotype 4 virus -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cbf | ||||||
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Title | Near-atomic resolution cryo-EM structure of Dengue serotype 4 virus | ||||||
Components |
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Keywords | VIRUS / FLAVIVIRUS | ||||||
Function / homology | Function and homology information flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral life cycle / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral life cycle / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / endoplasmic reticulum membrane / virion attachment to host cell / structural molecule activity / virion membrane / extracellular region / ATP binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | DENGUE VIRUS 2 DENGUE VIRUS 4 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN C, A, E, B, D, F | ||||||
Authors | Kostyuchenko, V.A. / Chew, P.L. / Ng, T.S. / Lok, S.M. | ||||||
Citation | Journal: J Virol / Year: 2014 Title: Near-atomic resolution cryo-electron microscopic structure of dengue serotype 4 virus. Authors: Victor A Kostyuchenko / Pau Ling Chew / Thiam-Seng Ng / Shee-Mei Lok / Abstract: Dengue virus (DENV), a mosquito-borne virus, is responsible for millions of cases of infections worldwide. There are four DENV serotypes (DENV1 to -4). After a primary DENV infection, the antibodies ...Dengue virus (DENV), a mosquito-borne virus, is responsible for millions of cases of infections worldwide. There are four DENV serotypes (DENV1 to -4). After a primary DENV infection, the antibodies elicited confer lifetime protection against that DENV serotype. However, in a secondary infection with another serotype, the preexisting antibodies may cause antibody-dependent enhancement (ADE) of infection of macrophage cells, leading to the development of the more severe form of disease, dengue hemorrhagic fever. Thus, a safe vaccine should stimulate protection against all dengue serotypes simultaneously. To facilitate the development of a vaccine, good knowledge of different DENV serotype structures is crucial. Structures of DENV1 and DENV2 had been solved previously. Here we present a near-atomic resolution cryo-electron microscopy (cryo-EM) structure of mature DENV4. Comparison of the DENV4 structure with similar-resolution cryo-EM structures of DENV1 and DENV2 showed differences in surface charge distribution, which may explain their differences in binding to cellular receptors, such as heparin. Also, observed variations in amino acid residues involved in interactions between envelope and membrane proteins on the virus surface correlate with their ability to undergo structural changes at higher temperatures. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4cbf.cif.gz | 66.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cbf.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cbf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4cbf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4cbf_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 4cbf_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/4cbf ftp://data.pdbj.org/pub/pdb/validation_reports/cb/4cbf | HTTPS FTP |
-Related structure data
Related structure data | 2485MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 54002.855 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DENGUE VIRUS 2 / Strain: THAILAND/NGS-C/1944 (DENV-2) / Cell line (production host): C6/36 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: E0WXI2 #2: Protein | Mass: 8242.602 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) DENGUE VIRUS 4 / References: UniProt: A4GV96, UniProt: E0WXI2*PLUS |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: MATURE DENGUE VIRUS SEROTYPE 4 / Type: VIRUS |
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Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Apr 14, 2012 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 125000 X / Calibrated magnification: 129629 X / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Temperature: 100 K |
Image recording | Electron dose: 18 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k) |
Image scans | Num. digital images: 716 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: EACH PARTICLE | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||
3D reconstruction | Method: CROSS-COMMON LINES / Resolution: 4.1 Å / Num. of particles: 16602 / Nominal pixel size: 1.08 Å / Actual pixel size: 1.08 Å / Magnification calibration: GRAPHITE SHEETS Details: MPSA SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2485. (DEPOSITION ID: 12027). Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: REAL SPACE CORRELATION / Details: METHOD--FLEXIBLE REFINEMENT PROTOCOL--CRYO-EM | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3J27 Accession code: 3J27 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||
Refinement | Highest resolution: 4.1 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4.1 Å
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