+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 : / negative regulation of innate immune response / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding ...: / negative regulation of innate immune response / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 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 / RNA helicase activity / host cell endoplasmic reticulum membrane / molecular adaptor activity / host cell perinuclear region of cytoplasm / membrane => GO:0016020 / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont entry into host cell / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / centrosome / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / GTP binding / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding / cytoplasm 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
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/5u4w ftp://data.pdbj.org/pub/pdb/validation_reports/u4/5u4w | HTTPS FTP |
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-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 FIELDBright-field microscopy |
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 |