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Yorodumi- EMDB-2073: Structure of the dengue virus glycoprotein non-structural protein... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2073 | |||||||||
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Title | Structure of the dengue virus glycoprotein non-structural protein 1 by electron microscopy and single-particle analysis | |||||||||
Map data | 3D reconstruction of recombinant DENV-2 sNS1 protein | |||||||||
Sample |
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Keywords | Flavivirus / Dengue / NS1 / glycoprotein | |||||||||
Function / homology | Flavivirus non-structural protein NS1 Function and homology information | |||||||||
Biological species | Dengue virus 2 | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 23.0 Å | |||||||||
Authors | Muller DA / Landsberg MJ / Bletchly C / Rothnagel R / Waddington L / Hankamer B / Young PR | |||||||||
Citation | Journal: J Gen Virol / Year: 2012 Title: Structure of the dengue virus glycoprotein non-structural protein 1 by electron microscopy and single-particle analysis. Authors: David A Muller / Michael J Landsberg / Cheryl Bletchly / Rosalba Rothnagel / Lynne Waddington / Ben Hankamer / Paul R Young / Abstract: The flavivirus non-structural protein 1 (NS1) is a glycoprotein that is secreted as a soluble hexameric complex during the course of natural infection. Growing evidence indicates that this secreted ...The flavivirus non-structural protein 1 (NS1) is a glycoprotein that is secreted as a soluble hexameric complex during the course of natural infection. Growing evidence indicates that this secreted form of NS1 (sNS1) plays a significant role in immune evasion and modulation during infection. Attempts to determine the crystal structure of NS1 have been unsuccessful to date and relatively little is known about the macromolecular organization of the sNS1 hexamer. Here, we have applied single-particle analysis to images of baculovirus-derived recombinant dengue 2 virus NS1 obtained by electron microscopy to determine its 3D structure to a resolution of 23 Å. This structure reveals a barrel-like organization of the three dimeric units that comprise the hexamer and provides further insights into the overall organization of oligomeric sNS1. | |||||||||
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_2073.map.gz | 1.2 MB | EMDB map data format | |
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Header (meta data) | emd-2073-v30.xml emd-2073.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_2073.jpg | 37.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2073 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2073 | HTTPS FTP |
-Validation report
Summary document | emd_2073_validation.pdf.gz | 200.1 KB | Display | EMDB validaton report |
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Full document | emd_2073_full_validation.pdf.gz | 199.3 KB | Display | |
Data in XML | emd_2073_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2073 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2073 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2073.map.gz / Format: CCP4 / Size: 4.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D reconstruction of recombinant DENV-2 sNS1 protein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.86 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 : Secreted form of DENV-2 NS1
Entire | Name: Secreted form of DENV-2 NS1 |
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Components |
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-Supramolecule #1000: Secreted form of DENV-2 NS1
Supramolecule | Name: Secreted form of DENV-2 NS1 / type: sample / ID: 1000 / Details: Monodisperse sample as assessed by SEC / Oligomeric state: Homohexamer / Number unique components: 1 |
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Molecular weight | Theoretical: 246 KDa |
-Macromolecule #1: Non structural protein 1
Macromolecule | Name: Non structural protein 1 / type: protein_or_peptide / ID: 1 / Name.synonym: NS1 / Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Dengue virus 2 / synonym: Dengue virus 2 / Location in cell: Secreted |
Molecular weight | Theoretical: 41 KDa |
Recombinant expression | Organism: Spodoptera (butterflies/moths) / Recombinant plasmid: pFastBac |
Sequence | InterPro: Flavivirus non-structural protein NS1 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 8 / Details: 20 mM Tris, 300 mM NaCl |
Staining | Type: NEGATIVE Details: Grids with adsorbed protein washed with an aqueous solution of 2% (w/v) uranyl acetate for 30 seconds. |
Grid | Details: 400 mesh copper grid with thin carbon support, glow discharged |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Temperature | Average: 295 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 93,000 times magnification |
Date | Sep 17, 2003 |
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: 40 / Average electron dose: 60 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 68000 |
Sample stage | Specimen holder: FEI single tilt room temperature / Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
Details | Particles selected semi-automatically using the SWARM-PS software |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, EMAN, XMIPP Details: An exhaustive evaluation of point symmetry was performed as described in the associated manuscript Number images used: 3523 |
Final two d classification | Number classes: 174 |