+Open data
-Basic information
Entry | Database: PDB / ID: 5ire | |||||||||
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Title | The cryo-EM structure of Zika Virus | |||||||||
Components |
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Keywords | VIRUS / 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 / membrane => GO:0016020 / 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 type I interferon-mediated signaling pathway / RNA helicase / 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: 3.8 Å | |||||||||
Authors | Sirohi, D. / Chen, Z. / Sun, L. / Klose, T. / Pierson, T. / Rossmann, M. / Kuhn, R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Science / Year: 2016 Title: The 3.8 Å resolution cryo-EM structure of Zika virus. Authors: Devika Sirohi / Zhenguo Chen / Lei Sun / Thomas Klose / Theodore C Pierson / Michael G Rossmann / Richard J Kuhn / Abstract: The recent rapid spread of Zika virus and its unexpected linkage to birth defects and an autoimmune neurological syndrome have generated worldwide concern. Zika virus is a flavivirus like the dengue, ...The recent rapid spread of Zika virus and its unexpected linkage to birth defects and an autoimmune neurological syndrome have generated worldwide concern. Zika virus is a flavivirus like the dengue, yellow fever, and West Nile viruses. We present the 3.8 angstrom resolution structure of mature Zika virus, determined by cryo-electron microscopy (cryo-EM). The structure of Zika virus is similar to other known flavivirus structures, except for the ~10 amino acids that surround the Asn(154) glycosylation site in each of the 180 envelope glycoproteins that make up the icosahedral shell. The carbohydrate moiety associated with this residue, which is recognizable in the cryo-EM electron density, may function as an attachment site of the virus to host cells. This region varies not only among Zika virus strains but also in other flaviviruses, which suggests that differences in this region may influence virus transmission and disease. | |||||||||
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 | 5ire.cif.gz | 302.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ire.ent.gz | 231 KB | Display | PDB format |
PDBx/mmJSON format | 5ire.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ire_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5ire_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5ire_validation.xml.gz | 72.1 KB | Display | |
Data in CIF | 5ire_validation.cif.gz | 106.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/5ire ftp://data.pdbj.org/pub/pdb/validation_reports/ir/5ire | HTTPS FTP |
-Related structure data
Related structure data | 8116MC 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 / Source: (natural) Zika virus / References: UniProt: A0A060H177, UniProt: A0A024B7W1*PLUS #2: Protein | Mass: 8496.883 Da / Num. of mol.: 3 / Fragment: UNP residues 179-253 / Source method: isolated from a natural source / Source: (natural) Zika virus / References: UniProt: A0A096XFQ2, UniProt: A0A024B7W1*PLUS #3: Polysaccharide | Source method: isolated from a genetically manipulated source |
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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 Details: Low passage Vero cells, derived from African green monkey kidney cells, were chosen for propagating the virus. Entity ID: #1-#2 / Source: MULTIPLE SOURCES | |||||||||||||||
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Source (natural) | Organism: Zika virus | |||||||||||||||
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION | |||||||||||||||
Natural host | Organism: Homo sapiens | |||||||||||||||
Virus shell | Name: capsid shell / Diameter: 490 nm / Triangulation number (T number): 3 | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: UC-A on holey carbon | |||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 298 K Details: Blot for 5 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3). |
-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 / Nominal magnification: 14000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 80 K |
Image recording | Average exposure time: 14 sec. / Electron dose: 23 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2974 |
Image scans | Sampling size: 1.04 µm / Width: 7420 / Height: 7676 / Movie frames/image: 70 / Used frames/image: 2-70 |
-Processing
EM software |
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Image processing | Details: The images were normalized. | ||||||||||||||||||||||||||||||||||||
CTF correction | Details: Phase flipping was performed during 3D reconstruction. Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 64518 Details: Particles were picked from 2-binned images using the template-picking method from Appion. | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11842 / Algorithm: FOURIER SPACE Details: Soft mark was applied to the even/odd map before FSC calculation. Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 150 / Protocol: AB INITIO MODEL / Space: REAL Target criteria: T = Tmap + weight * TrestraintsT = Tmap + weight * Trestraints |