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- EMDB-5103: Immature West Nile Virus (WNV) in complex with Fab fragments of t... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5103 | |||||||||
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Title | Immature West Nile Virus (WNV) in complex with Fab fragments of the anti-fusion loop antibody E53 | |||||||||
![]() | CryoEM reconstruction of immature West Nile Virus (WNV) in complex with Fab fragments of the anti-fusion loop antibody E53. | |||||||||
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![]() | West Nile Virus / WNV / immature / fusion loop / Fab / E53 | |||||||||
Function / homology | ![]() 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 / double-stranded RNA binding / viral capsid / 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 / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / symbiont entry into host cell / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / endoplasmic reticulum membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Immature West Nile Virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 15.0 Å | |||||||||
![]() | Cherrier MV / Kaufmann B / Nybakken GE / Lok SM / Warren JT / Nelson CA / Kostyuchenko VA / Holdaway HA / Chipman PR / Kuhn RJ ...Cherrier MV / Kaufmann B / Nybakken GE / Lok SM / Warren JT / Nelson CA / Kostyuchenko VA / Holdaway HA / Chipman PR / Kuhn RJ / Diamond MS / Rossmann MG / Fremont DH | |||||||||
![]() | ![]() 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 | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 15.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.1 KB 13.1 KB | Display Display | ![]() |
Images | ![]() | 380.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 365.2 KB | Display | ![]() |
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Full document | ![]() | 364.7 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ixxMC ![]() 5102C ![]() 3i50C ![]() 3ixyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | CryoEM reconstruction of immature West Nile Virus (WNV) in complex with Fab fragments of the anti-fusion loop antibody E53. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.69 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Immature West Nile Virus complexed with E53 Fab
Entire | Name: Immature West Nile Virus complexed with E53 Fab |
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Components |
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-Supramolecule #1000: Immature West Nile Virus complexed with E53 Fab
Supramolecule | Name: Immature West Nile Virus complexed with E53 Fab / type: sample / ID: 1000 Oligomeric state: T1 icosahedron with three E monomers and two Fab per asymmetric unit Number unique components: 2 |
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Molecular weight | Theoretical: 24.5 MDa |
-Supramolecule #1: Immature West Nile Virus
Supramolecule | Name: Immature West Nile Virus / type: virus / ID: 1 / Name.synonym: Immature West Nile Virus / Sci species name: Immature West Nile Virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: Immature West Nile Virus |
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Host (natural) | Organism: ![]() |
Molecular weight | Theoretical: 18.9 MDa |
Virus shell | Shell ID: 1 / Diameter: 600 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 / Details: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA |
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Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: Guillotine-style plunge freezeing device 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. |
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Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
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Temperature | Average: 98 K |
Alignment procedure | Legacy - Astigmatism: live FFT / Legacy - Electron beam tilt params: 0 |
Details | low dose. Two Imaging dates provided 25 MAR 2008 and 08-JAN-2008 |
Date | Jan 8, 2008 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 2.69 µm / Number real images: 84 / Average electron dose: 12.0 e/Å2 / Bits/pixel: 16 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 47244 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.859 µm / Nominal defocus min: 1.193 µm / Nominal magnification: 45000 |
Sample stage | Specimen holder: EUCENTRIC / Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
Details | 400 mesh copper grid |
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CTF correction | Details: Each particle |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider, XMIPP Details: Final maps were calculated from two averaged datasets Number images used: 3927 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: EMFIT |
Details | Protocol: Rigid Body. Each E molecule was divided into two rigid bodies, DI-DIII and DII-pr |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-3ixx: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: EMFIT |
Details | Protocol: Rigid Body. a model for WNV pr was generated by SWISS-MODEL based on DENV pr structure |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-3ixx: |