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Yorodumi- PDB-3ixx: The pseudo-atomic structure of West Nile immature virus in comple... -
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-Basic information
Entry | Database: PDB / ID: 3ixx | ||||||
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Title | The pseudo-atomic structure of West Nile immature virus in complex with Fab fragments of the anti-fusion loop antibody E53 | ||||||
Components |
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Keywords | VIRUS / West Nile Virus / WNV / immature / fusion loop / Fab / E53 / ATP-binding / Envelope protein / Helicase / Hydrolase / Membrane / Nucleotide-binding / RNA replication / Transmembrane / Virion / Icosahedral 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 / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 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 / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / 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 / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / endoplasmic reticulum membrane / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | West Nile virus Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15 Å | ||||||
Authors | Cherrier, M.V. / Kaufmann, B. / Nybakken, G.E. / Lok, S.M. / Warren, J.T. / Nelson, C.A. / Kostyuchenko, V.A. / Holdaway, H.A. / Chipman, P.R. / Kuhn, R.J. ...Cherrier, M.V. / Kaufmann, B. / Nybakken, G.E. / Lok, S.M. / Warren, J.T. / Nelson, C.A. / Kostyuchenko, V.A. / Holdaway, H.A. / Chipman, P.R. / Kuhn, R.J. / Diamond, M.S. / Rossmann, M.G. / Fremont, D.H. | ||||||
Citation | Journal: EMBO J / Year: 2009 Title: Structural basis for the preferential recognition of immature flaviviruses by a fusion-loop antibody. Authors: Mickaël V Cherrier / Bärbel Kaufmann / Grant E Nybakken / Shee-Mei Lok / Julia T Warren / Beverly R Chen / Christopher A Nelson / Victor A Kostyuchenko / Heather A Holdaway / Paul R ...Authors: Mickaël V Cherrier / Bärbel Kaufmann / Grant E Nybakken / Shee-Mei Lok / Julia T Warren / Beverly R Chen / Christopher A Nelson / Victor A Kostyuchenko / Heather A Holdaway / Paul R Chipman / Richard J Kuhn / Michael S Diamond / Michael G Rossmann / Daved H Fremont / Abstract: Flaviviruses are a group of human pathogens causing severe encephalitic or hemorrhagic diseases that include West Nile, dengue and yellow fever viruses. Here, using X-ray crystallography we have ...Flaviviruses are a group of human pathogens causing severe encephalitic or hemorrhagic diseases that include West Nile, dengue and yellow fever viruses. Here, using X-ray crystallography we have defined the structure of the flavivirus cross-reactive antibody E53 that engages the highly conserved fusion loop of the West Nile virus envelope glycoprotein. Using cryo-electron microscopy, we also determined that E53 Fab binds preferentially to spikes in noninfectious, immature flavivirions but is unable to bind significantly to mature virions, consistent with the limited solvent exposure of the epitope. We conclude that the neutralizing impact of E53 and likely similar fusion-loop-specific antibodies depends on its binding to the frequently observed immature component of flavivirus particles. Our results elucidate how fusion-loop antibodies, which comprise a significant fraction of the humoral response against flaviviruses, can function to control infection without appreciably recognizing mature virions. As these highly cross-reactive antibodies are often weakly neutralizing they also may contribute to antibody-dependent enhancement and flavi virus pathogenesis thereby complicating development of safe and effective vaccines. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3ixx.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ixx.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ixx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/3ixx ftp://data.pdbj.org/pub/pdb/validation_reports/ix/3ixx | HTTPS FTP |
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-Related structure data
Related structure data | 5103MC 5102C 3i50C 3ixyC 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
#1: Protein | Mass: 43272.098 Da / Num. of mol.: 3 / Fragment: West Nile Virus envelope protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) West Nile virus / Strain: NY99 / References: UniProt: Q9Q6P4, UniProt: A7TZT4*PLUS #2: Protein | Mass: 8742.004 Da / Num. of mol.: 3 / Fragment: West Nile Virus pr peptide Source method: isolated from a genetically manipulated source Source: (gene. exp.) West Nile virus / Strain: NY99 / References: UniProt: Q9WHD2, UniProt: Q3I100*PLUS #3: Antibody | Mass: 23630.504 Da / Num. of mol.: 2 / Fragment: E53 Fab Fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 #4: Antibody | Mass: 23588.107 Da / Num. of mol.: 2 / Fragment: E53 Fab Fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 |
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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 Virus complexed with E53 Fab / Type: VIRUS Details: T1 icosahedron with three E monomers and two Fab per asymmetric unit |
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Molecular weight | Value: 24.5 MDa / Experimental value: NO |
Details of virus | Empty: NO / Enveloped: YES / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Homo sapiens |
Buffer solution | pH: 8 / Details: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE 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 the 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 the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of 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 liquid nitrogen for later use in the microscope. |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/T / Date: Jan 8, 2008 / Details: low dose |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM / Electron beam tilt params: 0 |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 X / Calibrated magnification: 47244 X / Nominal defocus max: 2859 nm / Nominal defocus min: 1193 nm / Cs: 2 mm / Astigmatism: live FFT / Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: EUCENTRIC / Temperature: 98 K / Tilt angle max: -9999 ° / Tilt angle min: -9999 ° |
Image recording | Electron dose: 12 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: 15 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 3927 / Actual pixel size: 2.69 Å / Magnification calibration: 47244 Details: Final maps were calculated from two averaged datasets ( Details about the particle: 400 mesh copper grid ) Symmetry type: POINT | |||||||||||||||||||||
Atomic model building |
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Atomic model building |
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Refinement step | Cycle: LAST
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