+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6146 | |||||||||
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Title | Cryoelectron microscopy of dengue-Fab E104 complex at pH 5.5 | |||||||||
Map data | Reconstruction of low-pH Dengue virus complexed with DENV2 Fab E104 | |||||||||
Sample |
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Keywords | Dengue virus / DENV2 Fab E104 / Low pH / Fusion trimer | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / 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 type I interferon-mediated signaling pathway / RNA helicase / 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 | unidentified (others) / Dengue virus 2 Thailand/16681/84 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 26.0 Å | |||||||||
Authors | Zhang XZ / Sheng J / Austin SK / Hoornweg T / Smit JM / Kuhn RJ / Diamond MS / Rossmann MG | |||||||||
Citation | Journal: J Virol / Year: 2015 Title: Structure of acidic pH dengue virus showing the fusogenic glycoprotein trimers. Authors: Xinzheng Zhang / Ju Sheng / S Kyle Austin / Tabitha E Hoornweg / Jolanda M Smit / Richard J Kuhn / Michael S Diamond / Michael G Rossmann / Abstract: Flaviviruses undergo large conformational changes during their life cycle. Under acidic pH conditions, the mature virus forms transient fusogenic trimers of E glycoproteins that engage the lipid ...Flaviviruses undergo large conformational changes during their life cycle. Under acidic pH conditions, the mature virus forms transient fusogenic trimers of E glycoproteins that engage the lipid membrane in host cells to initiate viral fusion and nucleocapsid penetration into the cytoplasm. However, the dynamic nature of the fusogenic trimer has made the determination of its structure a challenge. Here we have used Fab fragments of the neutralizing antibody DV2-E104 to stop the conformational change of dengue virus at an intermediate stage of the fusion process. Using cryo-electron microscopy, we show that in this intermediate stage, the E glycoproteins form 60 trimers that are similar to the predicted "open" fusogenic trimer. IMPORTANCE: The structure of a dengue virus has been captured during the formation of fusogenic trimers. This was accomplished by binding Fab fragments of the neutralizing antibody DV2-E104 to the ...IMPORTANCE: The structure of a dengue virus has been captured during the formation of fusogenic trimers. This was accomplished by binding Fab fragments of the neutralizing antibody DV2-E104 to the virus at neutral pH and then decreasing the pH to 5.5. These trimers had an "open" conformation, which is distinct from the "closed" conformation of postfusion trimers. Only two of the three E proteins within each spike are bound by a Fab molecule at domain III. Steric hindrance around the icosahedral 3-fold axes prevents binding of a Fab to the third domain III of each E protein spike. Binding of the DV2-E104 Fab fragments prevents domain III from rotating by about 130° to the postfusion orientation and thus precludes the stem region from "zipping" together the three E proteins along the domain II boundaries into the "closed" postfusion conformation, thus inhibiting fusion. | |||||||||
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_6146.map.gz | 14.4 MB | EMDB map data format | |
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Header (meta data) | emd-6146-v30.xml emd-6146.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | 400_6146.gif 80_6146.gif | 63.1 KB 4.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6146 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6146 | HTTPS FTP |
-Validation report
Summary document | emd_6146_validation.pdf.gz | 344.7 KB | Display | EMDB validaton report |
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Full document | emd_6146_full_validation.pdf.gz | 344.2 KB | Display | |
Data in XML | emd_6146_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6146 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6146 | HTTPS FTP |
-Related structure data
Related structure data | 3j8dMC 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_6146.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of low-pH Dengue virus complexed with DENV2 Fab E104 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.2 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 : Dengue virus complexed with Fab E104 at pH 5.5
Entire | Name: Dengue virus complexed with Fab E104 at pH 5.5 |
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Components |
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-Supramolecule #1000: Dengue virus complexed with Fab E104 at pH 5.5
Supramolecule | Name: Dengue virus complexed with Fab E104 at pH 5.5 / type: sample / ID: 1000 / Number unique components: 2 |
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-Supramolecule #1: Dengue virus 2 Thailand/16681/84
Supramolecule | Name: Dengue virus 2 Thailand/16681/84 / type: virus / ID: 1 / NCBI-ID: 31634 / Sci species name: Dengue virus 2 Thailand/16681/84 / Sci species strain: 16681 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Host system | Organism: unidentified (others) |
Virus shell | Shell ID: 1 / Name: E / Diameter: 600 Å / T number (triangulation number): 3 |
-Macromolecule #1: Fab E104
Macromolecule | Name: Fab E104 / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: unidentified (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 5.5 / Details: 120 mM NaCl, 20 mM Tris HCl, 1 mM EDTA |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Jan 1, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 1000 / Average electron dose: 24 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: OTHER / Software - Name: EMAN / Number images used: 528 |
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-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: EMFit |
Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT |
Output model | PDB-3j8d: |