+Open data
-Basic information
Entry | Database: PDB / ID: 3j0b | ||||||
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Title | cryo-EM reconstruction of West Nile virus | ||||||
Components | envelope glycoprotein E | ||||||
Keywords | VIRUS / West Nile Virus | ||||||
Function / homology | Function and homology information 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 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase 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 / 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 / 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: 10.3 Å | ||||||
Authors | Zhang, W. / Kaufmann, B. / Chipman, P.R. / Kuhn, R.J. / Rossmann, M.G. | ||||||
Citation | Journal: J Struct Biol / Year: 2013 Title: Membrane curvature in flaviviruses. Authors: Wei Zhang / Bärbel Kaufmann / Paul R Chipman / Richard J Kuhn / Michael G Rossmann / Abstract: Coordinated interplay between membrane proteins and the lipid bilayer is required for such processes as transporter function and the entrance of enveloped viruses into host cells. In this study, ...Coordinated interplay between membrane proteins and the lipid bilayer is required for such processes as transporter function and the entrance of enveloped viruses into host cells. In this study, three-dimensional cryo-electron microscopy density maps of mature and immature flaviviruses were analyzed to assess the curvature of the membrane leaflets and its relation to membrane-bound viral glycoproteins. The overall morphology of the viral membrane is determined by the icosahedral scaffold composed of envelope (E) and membrane (M) proteins through interaction of the proteins' stem-anchor regions with the membrane. In localized regions, small membrane areas exhibit convex, concave, flat or saddle-shaped surfaces that are constrained by the specific protein organization within each membrane leaflet. These results suggest that the organization of membrane proteins in small enveloped viruses mediate the formation of membrane curvature. | ||||||
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 | 3j0b.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j0b.ent.gz | 30 KB | Display | PDB format |
PDBx/mmJSON format | 3j0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j0b_validation.pdf.gz | 804.5 KB | Display | wwPDB validaton report |
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Full document | 3j0b_full_validation.pdf.gz | 806 KB | Display | |
Data in XML | 3j0b_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 3j0b_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/3j0b ftp://data.pdbj.org/pub/pdb/validation_reports/j0/3j0b | HTTPS FTP |
-Related structure data
Related structure data | 5296MC 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: 43272.098 Da / Num. of mol.: 3 / Fragment: UNP residues 291-690 / Source method: isolated from a natural source / Source: (natural) West Nile virus / References: UniProt: Q9Q6P4 |
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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: West Nile Virus / Type: VIRUS |
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Details of virus | Empty: NO / Enveloped: YES / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION |
Buffer solution | Name: TNE (12 mM Tris, 120 mM NaCl, 1 mM EDTA) / pH: 8 / Details: 12 mM Tris-HCL, 120 mM NaCl, 1 mM EDTA |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 12 mM Tris-HCL, 120 mM NaCl, 1 mM EDTA |
Specimen support | Details: 400 mesh holey carbon copper grid |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 98 K / Details: vitrification carried out in a BSL3 lab Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by means of fine ...Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be melted slightly. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot off excess buffer sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen and the grid is transferred under liquid nitrogen to a storage box immersed in liquid nitrogen for later use in the microscope. |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/T / Date: Oct 21, 2004 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 47440 X / Nominal defocus max: 321 nm / Nominal defocus min: 112 nm / Cs: 2 mm / Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Eucentric / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: each particle | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Resolution: 10.3 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 1556 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: 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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