+Open data
-Basic information
Entry | Database: PDB / ID: 2of6 | ||||||
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Title | Structure of immature West Nile virus | ||||||
Components | envelope glycoprotein E | ||||||
Keywords | VIRUS / EM immature flavivirus West Nile / icosahedral virus | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 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 / 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 / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | West Nile virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 24 Å | ||||||
Authors | Zhang, Y. / Kaufmann, B. / Chipman, P.R. / Kuhn, R.J. / Rossmann, M.G. | ||||||
Citation | Journal: J Virol / Year: 2007 Title: Structure of immature West Nile virus. Authors: Ying Zhang / Bärbel Kaufmann / Paul R Chipman / Richard J Kuhn / Michael G Rossmann / Abstract: The structure of immature West Nile virus particles, propagated in the presence of ammonium chloride to block virus maturation in the low-pH environment of the trans-Golgi network, was determined by ...The structure of immature West Nile virus particles, propagated in the presence of ammonium chloride to block virus maturation in the low-pH environment of the trans-Golgi network, was determined by cryo-electron microscopy (cryo-EM). The structure of these particles was similar to that of immature West Nile virus particles found as a minor component of mature virus samples (naturally occurring immature particles [NOIPs]). The structures of mature infectious flaviviruses are radically different from those of the immature particles. The similarity of the ammonium chloride-treated particles and NOIPs suggests either that the NOIPs have not undergone any conformational change during maturation or that the conformational change is reversible. Comparison with the cryo-EM reconstruction of immature dengue virus established the locations of the N-linked glycosylation sites of these viruses, verifying the interpretation of the reconstructions of the immature flaviviruses. | ||||||
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 | 2of6.cif.gz | 49.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2of6.ent.gz | 30 KB | Display | PDB format |
PDBx/mmJSON format | 2of6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2of6_validation.pdf.gz | 795.1 KB | Display | wwPDB validaton report |
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Full document | 2of6_full_validation.pdf.gz | 794.7 KB | Display | |
Data in XML | 2of6_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 2of6_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/2of6 ftp://data.pdbj.org/pub/pdb/validation_reports/of/2of6 | HTTPS FTP |
-Related structure data
Related structure data | 1314MC 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: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 43272.098 Da / Num. of mol.: 3 / Fragment: N-terminal 400 residues / Source method: isolated from a natural source / Source: (natural) West Nile virus / Genus: Flavivirus / Strain: NY99 / References: UniProt: Q9Q6P4, UniProt: P14335*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: immature West Nile / Type: VIRUS |
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Details of virus | Host category: INVERTEBRATES AND VERTEBRATES / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Chlorocebus aethiops / Strain: Vero cells |
Buffer solution | Name: 12mM Tris, 120mM NaCl, 1mM EDTA / pH: 8 / Details: 12mM Tris, 120mM NaCl, 1mM EDTA |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: This grid plus sample was kept at -170 deg C for a month before taking pictures |
Vitrification | Cryogen name: ETHANE / Details: rapidly frozen by plunging into an ethane slush |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/T / Date: Mar 15, 2006 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 47400 X / Nominal defocus max: 3100 nm / Nominal defocus min: 1300 nm / Cs: 2 mm |
Specimen holder | Temperature: 87 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 22 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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CTF correction | Details: CTF correction of each particle | ||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||
3D reconstruction | Method: PFT / Resolution: 24 Å / Num. of particles: 341 / Actual pixel size: 2.95 Å / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Target criteria: best fit using criterial described in paper by Rossmann et al., Journal of structural biology 136, 190-200 (2001) Details: METHOD--Three E molecules were fitted consecutively REFINEMENT PROTOCOL--rigid body | ||||||||||||||||||||
Atomic model building | PDB-ID: 2HG0 Accession code: 2HG0 / Source name: PDB / Type: experimental model | ||||||||||||||||||||
Refinement step | Cycle: LAST
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