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Yorodumi- EMDB-5190: West Nile Virus in complex with Fab fragments of the neutralizing... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5190 | |||||||||
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Title | West Nile Virus in complex with Fab fragments of the neutralizing monoclonal antibody CR4354 | |||||||||
Map data | CryoEM map of West Nile virus in complex with Fab fragments of the neutralizing antibody CR4354 | |||||||||
Sample |
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Keywords | West Nile Virus / infectious virus / flavivirus / neutralizing antibody / Fab fragment / CR4354 / complex / envelope protein | |||||||||
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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / 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 / nucleoside-triphosphate phosphatase / viral capsid / 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 / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / induction by virus of host autophagy / symbiont entry into host cell / 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 / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / West Nile virus HNY99 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.7 Å | |||||||||
Authors | Kaufmann B / Vogt MR / Holdaway HA / Goudsmit J / Chipman PR / Kuhn RJ / Diamond MS / Rossmann MG | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2010 Title: Neutralization of West Nile virus by cross-linking of its surface proteins with Fab fragments of the human monoclonal antibody CR4354. Authors: Bärbel Kaufmann / Matthew R Vogt / Jaap Goudsmit / Heather A Holdaway / Anastasia A Aksyuk / Paul R Chipman / Richard J Kuhn / Michael S Diamond / Michael G Rossmann / Abstract: Many flaviviruses are significant human pathogens, with the humoral immune response playing an essential role in restricting infection and disease. CR4354, a human monoclonal antibody isolated from a ...Many flaviviruses are significant human pathogens, with the humoral immune response playing an essential role in restricting infection and disease. CR4354, a human monoclonal antibody isolated from a patient, neutralizes West Nile virus (WNV) infection at a postattachment stage in the viral life-cycle. Here, we determined the structure of WNV complexed with Fab fragments of CR4354 using cryoelectron microscopy. The outer glycoprotein shell of a mature WNV particle is formed by 30 rafts of three homodimers of the viral surface protein E. CR4354 binds to a discontinuous epitope formed by protein segments from two neighboring E molecules, but does not cause any detectable structural disturbance on the viral surface. The epitope occurs at two independent positions within an icosahedral asymmetric unit, resulting in 120 binding sites on the viral surface. The cross-linking of the six E monomers within one raft by four CR4354 Fab fragments suggests that the antibody neutralizes WNV by blocking the pH-induced rearrangement of the E protein required for virus fusion with the endosomal membrane. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5190.map.gz | 37.9 MB | EMDB map data format | |
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Header (meta data) | emd-5190-v30.xml emd-5190.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
Images | emd_5190_1.jpg | 116.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5190 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5190 | HTTPS FTP |
-Validation report
Summary document | emd_5190_validation.pdf.gz | 304.9 KB | Display | EMDB validaton report |
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Full document | emd_5190_full_validation.pdf.gz | 304.5 KB | Display | |
Data in XML | emd_5190_validation.xml.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5190 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5190 | HTTPS FTP |
-Related structure data
Related structure data | 3iywMC 3n9gC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5190.map.gz / Format: CCP4 / Size: 99.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of West Nile virus in complex with Fab fragments of the neutralizing antibody CR4354 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.7237 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : West Nile virus NY99 complexed with Fab fragments of the neutrali...
Entire | Name: West Nile virus NY99 complexed with Fab fragments of the neutralizing monoclonal antibody CR4354 |
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Components |
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-Supramolecule #1000: West Nile virus NY99 complexed with Fab fragments of the neutrali...
Supramolecule | Name: West Nile virus NY99 complexed with Fab fragments of the neutralizing monoclonal antibody CR4354 type: sample / ID: 1000 Details: complex was formed by incubating infectious virus with Fab (ratio of about 4 Fab fragments per E molecule) at 37degC for 30min, followed by a 2h incubation at RT 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: 23 MDa |
-Supramolecule #1: West Nile virus HNY99
Supramolecule | Name: West Nile virus HNY99 / type: virus / ID: 1 / Name.synonym: West Nile virus Details: The infectious virus (180 molecules of envelope glycoprotein E form outer protein shell of virion) is complexed with Fab fragments of the neutralizing antibody CR4354 (120 Fab molecules per virion) Sci species name: West Nile virus HNY99 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: West Nile virus |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Molecular weight | Theoretical: 17 MDa |
Virus shell | Shell ID: 1 / Name: E protein shell / Diameter: 495 Å / T number (triangulation number): 1 |
-Macromolecule #1: CR4354 Fab fragment
Macromolecule | Name: CR4354 Fab fragment / type: protein_or_peptide / ID: 1 / Name.synonym: CR4354 Fab fragment Details: Fab fragments of the neutralizing monoclonal antibody CR4354 are complexed with West Nile Virus (120 Fab molecules per virion) Number of copies: 120 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Tissue: peripheral blood / Cell: B cells |
Molecular weight | Theoretical: 50 KDa |
Recombinant expression | Organism: mammalian cells (unknown) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 / Details: 12mM Tris-HCl, 120mM NaCl, 1mM EDTA |
Grid | Details: holey carbon 400 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: guillotine-style plunge freezing 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. |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
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Temperature | Average: 98 K |
Alignment procedure | Legacy - Astigmatism: live FFT at 200K magnification |
Details | low dose imaging |
Date | Sep 9, 2009 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 69 / Average electron dose: 22 e/Å2 / Details: scanned images binned 2x2 / Od range: 1 / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 47244 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.53 µm / Nominal defocus min: 1.45 µm / Nominal magnification: 45000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | The particles were selected interactively at the computer terminal. |
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CTF correction | Details: Each particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM Details: final map includes data to 13.0 Ang resolution (FCS at about 0.2 cut-off) Number images used: 5006 |