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Yorodumi- PDB-5iz7: Cryo-EM structure of thermally stable Zika virus strain H/PF/2013 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iz7 | ||||||||||||
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Title | Cryo-EM structure of thermally stable Zika virus strain H/PF/2013 | ||||||||||||
Components |
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Keywords | VIRUS / viral protein / flavivirus / glycoprotein / zika virus | ||||||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / 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 / molecular adaptor activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / symbiont entry into host cell / induction by virus of host autophagy / serine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / centrosome / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell nucleus / virion attachment to host cell / GTP binding / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Zika virus | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Kostyuchenko, V.A. / Zhang, S. / Fibriansah, G. / Lok, S.M. | ||||||||||||
Funding support | Singapore, 3items
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Citation | Journal: Nature / Year: 2016 Title: Structure of the thermally stable Zika virus. Authors: Victor A Kostyuchenko / Elisa X Y Lim / Shuijun Zhang / Guntur Fibriansah / Thiam-Seng Ng / Justin S G Ooi / Jian Shi / Shee-Mei Lok / Abstract: Zika virus (ZIKV), formerly a neglected pathogen, has recently been associated with microcephaly in fetuses, and with Guillian-Barré syndrome in adults. Here we present the 3.7 Å resolution cryo- ...Zika virus (ZIKV), formerly a neglected pathogen, has recently been associated with microcephaly in fetuses, and with Guillian-Barré syndrome in adults. Here we present the 3.7 Å resolution cryo-electron microscopy structure of ZIKV, and show that the overall architecture of the virus is similar to that of other flaviviruses. Sequence and structural comparisons of the ZIKV envelope (E) protein with other flaviviruses show that parts of the E protein closely resemble the neurovirulent West Nile and Japanese encephalitis viruses, while others are similar to dengue virus (DENV). However, the contribution of the E protein to flavivirus pathobiology is currently not understood. The virus particle was observed to be structurally stable even when incubated at 40 °C, in sharp contrast to the less thermally stable DENV. This is also reflected in the infectivity of ZIKV compared to DENV serotypes 2 and 4 (DENV2 and DENV4) at different temperatures. The cryo-electron microscopy structure shows a virus with a more compact surface. This structural stability of the virus may help it to survive in the harsh conditions of semen, saliva and urine. Antibodies or drugs that destabilize the structure may help to reduce the disease outcome or limit the spread of the virus. | ||||||||||||
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 | 5iz7.cif.gz | 333.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iz7.ent.gz | 268.9 KB | Display | PDB format |
PDBx/mmJSON format | 5iz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iz7_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5iz7_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5iz7_validation.xml.gz | 83.6 KB | Display | |
Data in CIF | 5iz7_validation.cif.gz | 118.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/5iz7 ftp://data.pdbj.org/pub/pdb/validation_reports/iz/5iz7 | HTTPS FTP |
-Related structure data
Related structure data | 8139MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 54444.051 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: glycosylated at N154 / Source: (natural) Zika virus / Cell line: C6/36 / Strain: H/PF/2013 / References: UniProt: A0A024B7W1 #2: Protein | Mass: 8496.883 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Zika virus / Cell line: C6/36 / Strain: H/PF/2013 / References: UniProt: A0A0U4DG08, UniProt: A0A024B7W1*PLUS #3: Sugar | |
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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: Zika virus / Type: VIRUS / Entity ID: #1-#2 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 10 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Zika virus / Strain: H/PF/2013 | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION | ||||||||||||||||||||
Natural host | Organism: Homo sapiens | ||||||||||||||||||||
Virus shell | Name: glycoprotein shell / Diameter: 480 nm / Triangulation number (T number): 1 | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: purified with PEG precipitation, sucrose cushion and potassium tartrate gradient | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: blot for 1s |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Image recording | Average exposure time: 1.8 sec. / Electron dose: 50 e/Å2 / Detector mode: OTHER / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3086 |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 30 / Used frames/image: 2-11 |
-Processing
EM software |
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Image processing | Details: images collected in movie mode, 30 frames per 1.8s exposure; frames aligned with MotionCorr, frames 2-11 averaged to produce images for further processing | ||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: correction for astigmatism included / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 11600 / Details: manually picked | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7180 / Algorithm: FOURIER SPACE / Num. of class averages: 7180 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: RECIPROCAL / Target criteria: residual Details: Only icosahedral symmetry imposed. Rwork 0.323 Rtest 0.324 | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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