+Open data
-Basic information
Entry | Database: PDB / ID: 5u4w | |||||||||
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Title | Cryo-EM Structure of Immature Zika Virus | |||||||||
Components |
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Keywords | VIRUS / immature Zika virus / viral protein | |||||||||
Function / homology | Function and homology information : / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid ...: / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / 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 / host cell surface / 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 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: 9.1 Å | |||||||||
Authors | Mangala Prasad, V. / Miller, A.S. / Klose, T. / Sirohi, D. / Buda, G. / Jiang, W. / Kuhn, R.J. / Rossmann, M.G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Struct Mol Biol / Year: 2017 Title: Structure of the immature Zika virus at 9 Å resolution. Authors: Vidya Mangala Prasad / Andrew S Miller / Thomas Klose / Devika Sirohi / Geeta Buda / Wen Jiang / Richard J Kuhn / Michael G Rossmann / Abstract: The current Zika virus (ZIKV) epidemic is characterized by severe pathogenicity in both children and adults. Sequence changes in ZIKV since its first isolation are apparent when pre-epidemic strains ...The current Zika virus (ZIKV) epidemic is characterized by severe pathogenicity in both children and adults. Sequence changes in ZIKV since its first isolation are apparent when pre-epidemic strains are compared with those causing the current epidemic. However, the residues that are responsible for ZIKV pathogenicity are largely unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of the immature ZIKV at 9-Å resolution. The cryo-EM map was fitted with the crystal structures of the precursor membrane and envelope glycoproteins and was shown to be similar to the structures of other known immature flaviviruses. However, the immature ZIKV contains a partially ordered capsid protein shell that is less prominent in other immature flaviviruses. Furthermore, six amino acids near the interface between pr domains at the top of the spikes were found to be different between the pre-epidemic and epidemic ZIKV, possibly influencing the composition and structure of the resulting viruses. | |||||||||
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 | 5u4w.cif.gz | 341.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u4w.ent.gz | 277.8 KB | Display | PDB format |
PDBx/mmJSON format | 5u4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u4w_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5u4w_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5u4w_validation.xml.gz | 69.1 KB | Display | |
Data in CIF | 5u4w_validation.cif.gz | 99.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/5u4w ftp://data.pdbj.org/pub/pdb/validation_reports/u4/5u4w | HTTPS FTP |
-Related structure data
Related structure data | 8508MC 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
-Protein , 4 types, 12 molecules ACEBDFGIKHJL
#1: Protein | Mass: 44801.410 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: O11875*PLUS #2: Protein | Mass: 9261.531 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: A0A0B4L3F2*PLUS #3: Protein | Mass: 6892.228 Da / Num. of mol.: 3 / Fragment: transmembrane domain (UNP residues 726-791) / Source method: isolated from a natural source / Source: (natural) Zika virus / References: UniProt: A0A1B2ZC85, UniProt: A0A024B7W1*PLUS #4: Protein | Mass: 5984.065 Da / Num. of mol.: 3 / Fragment: transmembrane domain (UNP residues 238-290) / Source method: isolated from a natural source / Source: (natural) Zika virus / References: UniProt: A0A142I5B9, UniProt: A0A024B7W1*PLUS |
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-Sugars , 2 types, 18 molecules
#5: Sugar | ChemComp-NAG / #6: Sugar | ChemComp-BMA / |
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-Details
Sequence details | The sample was from Zika virus, but the modeled sequences for chains A, B, C, D, E, and F are from ...The sample was from Zika virus, but the modeled sequences for chains A, B, C, D, E, and F are from Dengue virus. |
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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 |
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Source (natural) |
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Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION | ||||||||||||||||||||
Natural host | Organism: Homo sapiens | ||||||||||||||||||||
Virus shell | Name: prM-E glycoprotein / Diameter: 600 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 | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Ultrathin carbon | ||||||||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 7.6 sec. / Electron dose: 4.7 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3341 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 14351 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9315 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient |