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- EMDB-5674: Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5674 | |||||||||
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Title | Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody | |||||||||
![]() | Reconstruction of immature Dengue virus complexed with high-concentration 2H2 Fab at pH 7 | |||||||||
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![]() | Dengue Maturation Immature Dengue Antibody | |||||||||
Function / homology | ![]() immunoglobulin complex / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / immunoglobulin complex, circulating / immunoglobulin receptor binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / complement activation, classical pathway / antigen binding ...immunoglobulin complex / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / immunoglobulin complex, circulating / immunoglobulin receptor binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / complement activation, classical pathway / antigen binding / double-stranded RNA binding / viral capsid / protein complex oligomerization / monoatomic ion channel activity / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / adaptive immune response / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / blood microparticle / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / immune response / 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 / virion membrane / structural molecule activity / proteolysis / extracellular space / extracellular exosome / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 21.0 Å | |||||||||
![]() | Wang Z / Li L / Penningtona JG / Sheng J / Yap M / Plevk P / Meng G / Sun L / Jiang W / Rossmann MG | |||||||||
![]() | ![]() Title: Obstruction of dengue virus maturation by Fab fragments of the 2H2 antibody. Authors: Zhiqing Wang / Long Li / Janice G Pennington / Ju Sheng / Moh Lan Yap / Pavel Plevka / Geng Meng / Lei Sun / Wen Jiang / Michael G Rossmann / ![]() Abstract: The 2H2 monoclonal antibody recognizes the precursor peptide on immature dengue virus and might therefore be a useful tool for investigating the conformational change that occurs when the immature ...The 2H2 monoclonal antibody recognizes the precursor peptide on immature dengue virus and might therefore be a useful tool for investigating the conformational change that occurs when the immature virus enters an acidic environment. During dengue virus maturation, spiky, immature, noninfectious virions change their structure to form smooth-surfaced particles in the slightly acidic environment of the trans-Golgi network, thereby allowing cellular furin to cleave the precursor-membrane proteins. The dengue virions become fully infectious when they release the cleaved precursor peptide upon reaching the neutral-pH environment of the extracellular space. Here we report on the cryo-electron microscopy structures of the immature virus complexed with the 2H2 antigen binding fragments (Fab) at different concentrations and under various pH conditions. At neutral pH and a high concentration of Fab molecules, three Fab molecules bind to three precursor-membrane proteins on each spike of the immature virus. However, at a low concentration of Fab molecules and pH 7.0, only two Fab molecules bind to each spike. Changing to a slightly acidic pH caused no detectable change of structure for the sample with a high Fab concentration but caused severe structural damage to the low-concentration sample. Therefore, the 2H2 Fab inhibits the maturation process of immature dengue virus when Fab molecules are present at a high concentration, because the three Fab molecules on each spike hold the precursor-membrane molecules together, thereby inhibiting the normal conformational change that occurs during maturation. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 39.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.5 KB 11.5 KB | Display Display | ![]() |
Images | ![]() | 187.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 369.4 KB | Display | ![]() |
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Full document | ![]() | 369 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3j42MC ![]() 5675C ![]() 5676C ![]() 5677C ![]() 4kvcC C: citing same article ( M: atomic model generated by this map |
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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 | Reconstruction of immature Dengue virus complexed with high-concentration 2H2 Fab at pH 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.72 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 : High-concentration Fab Fragment of 2H2 antibody binding to immatu...
Entire | Name: High-concentration Fab Fragment of 2H2 antibody binding to immature Dengue virus at pH 7 |
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Components |
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-Supramolecule #1000: High-concentration Fab Fragment of 2H2 antibody binding to immatu...
Supramolecule | Name: High-concentration Fab Fragment of 2H2 antibody binding to immature Dengue virus at pH 7 type: sample / ID: 1000 Oligomeric state: Three Fab fragments bind to three pr on each trimeric spike Number unique components: 3 |
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-Supramolecule #1: Dengue virus
Supramolecule | Name: Dengue virus / type: virus / ID: 1 / Details: immature virus / NCBI-ID: 12637 / Sci species name: Dengue virus / Sci species strain: P16881 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() |
Virus shell | Shell ID: 1 / Name: prM and E / Diameter: 600 Å / T number (triangulation number): 3 |
-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: 7 / Details: 100mM phosphate buffer |
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Grid | Details: Quantifoil 200 mesh |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER |
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Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Temperature | Min: 80 K / Max: 105 K / Average: 100 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Date | Apr 7, 2011 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON COOLSCAN / Digitization - Sampling interval: 6 µm / Number real images: 49 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 51040 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
CTF correction | Details: Film |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: JSPR, EMAN2, EMAN / Number images used: 378 |