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Yorodumi- PDB-3i50: Crystal structure of the West Nile Virus envelope glycoprotein in... -
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-Basic information
Entry | Database: PDB / ID: 3i50 | ||||||
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Title | Crystal structure of the West Nile Virus envelope glycoprotein in complex with the E53 antibody Fab | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / ANTIBODY / FAB / VIRUS / ENVELOPE / IMMUNOGLOBULIN / FUSION LOOP / Disulfide bond / Envelope protein / Membrane / Transmembrane / Virion / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
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 / 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 Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Nybakken, G.E. / Warren, J.T. / Chen, B.R. / Nelson, C.A. / 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i50.cif.gz | 283.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i50.ent.gz | 240.8 KB | Display | PDB format |
PDBx/mmJSON format | 3i50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i50_validation.pdf.gz | 447.1 KB | Display | wwPDB validaton report |
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Full document | 3i50_full_validation.pdf.gz | 480.8 KB | Display | |
Data in XML | 3i50_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 3i50_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/3i50 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/3i50 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43416.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) West Nile virus / Strain: NY 1999 / Gene: ENVELOPE / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q91R02, UniProt: Q9Q6P4*PLUS |
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#2: Antibody | Mass: 22577.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Description: B-cell hybridoma cells / Cell: hybridoma / Gene: Light chain of E53 antibody / Production host: Mus musculus (house mouse) |
#3: Antibody | Mass: 23665.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Description: B-cell hybridoma cells / Cell: hybridoma / Gene: Heavy chain of E53 antibody / Production host: Mus musculus (house mouse) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG 300, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.24 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Jun 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 3→50.15 Å / Num. all: 21544 / Num. obs: 21428 / % possible obs: 99.5 % / Redundancy: 4.45 % / Biso Wilson estimate: 110.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 4.39 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2 / Num. unique all: 2119 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.98 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 91.349 Å2 / ksol: 0.307 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 321.43 Å2 / Biso mean: 146.439 Å2 / Biso min: 42.65 Å2
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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