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Yorodumi- EMDB-23045: Chimeric flavivirus between Binjari virus and Murray Valley encep... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23045 | |||||||||
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Title | Chimeric flavivirus between Binjari virus and Murray Valley encephalitis virus | |||||||||
Map data | Local resolution filtered map | |||||||||
Sample |
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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 / clathrin-dependent endocytosis of virus by host cell ...: / 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 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Murray Valley encephalitis virus / Binjari virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Hardy JM / Venugopal HV / Newton ND / Watterson D / Coulibaly FJ | |||||||||
Funding support | Australia, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: A unified route for flavivirus structures uncovers essential pocket factors conserved across pathogenic viruses. Authors: Joshua M Hardy / Natalee D Newton / Naphak Modhiran / Connor A P Scott / Hariprasad Venugopal / Laura J Vet / Paul R Young / Roy A Hall / Jody Hobson-Peters / Fasséli Coulibaly / Daniel Watterson / Abstract: The epidemic emergence of relatively rare and geographically isolated flaviviruses adds to the ongoing disease burden of viruses such as dengue. Structural analysis is key to understand and combat ...The epidemic emergence of relatively rare and geographically isolated flaviviruses adds to the ongoing disease burden of viruses such as dengue. Structural analysis is key to understand and combat these pathogens. Here, we present a chimeric platform based on an insect-specific flavivirus for the safe and rapid structural analysis of pathogenic viruses. We use this approach to resolve the architecture of two neurotropic viruses and a structure of dengue virus at 2.5 Å, the highest resolution for an enveloped virion. These reconstructions allow improved modelling of the stem region of the envelope protein, revealing two lipid-like ligands within highly conserved pockets. We show that these sites are essential for viral growth and important for viral maturation. These findings define a hallmark of flavivirus virions and a potential target for broad-spectrum antivirals and vaccine design. We anticipate the chimeric platform to be widely applicable for investigating flavivirus biology. | |||||||||
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_23045.map.gz | 440.6 MB | EMDB map data format | |
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Header (meta data) | emd-23045-v30.xml emd-23045.xml | 28.6 KB 28.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23045_fsc.xml | 21.2 KB | Display | FSC data file |
Images | emd_23045.png | 293.2 KB | ||
Masks | emd_23045_msk_1.map | 824 MB | Mask map | |
Others | emd_23045_additional_1.map.gz emd_23045_additional_2.map.gz emd_23045_additional_3.map.gz emd_23045_half_map_1.map.gz emd_23045_half_map_2.map.gz | 647.3 MB 216.1 MB 745.1 MB 660.7 MB 660.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23045 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23045 | HTTPS FTP |
-Related structure data
Related structure data | 7kvbMC 7kv8C 7kv9C 7kvaC C: citing same article (ref.) M: atomic model generated by this map |
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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_23045.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Local resolution filtered map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.046 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23045_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unmasked unsharpened map
File | emd_23045_additional_1.map | ||||||||||||
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Annotation | Unmasked unsharpened map | ||||||||||||
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Density Histograms |
-Additional map: Masked sharpened map
File | emd_23045_additional_2.map | ||||||||||||
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Annotation | Masked sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unmasked sharpened map
File | emd_23045_additional_3.map | ||||||||||||
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Annotation | Unmasked sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_23045_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_23045_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Binjari virus
Entire | Name: Binjari virus |
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Components |
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-Supramolecule #1: Binjari virus
Supramolecule | Name: Binjari virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Aedes albopictus C6/36 cells / NCBI-ID: 2305258 / Sci species name: Binjari virus / Sci species strain: BFTA20 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Ochlerotatus normanensis (mosquito) |
Molecular weight | Theoretical: 11.2 MDa |
Virus shell | Shell ID: 1 / Diameter: 470.0 Å / T number (triangulation number): 3 |
-Supramolecule #2: M and E from Murray Valley encephalitis virus strain MVE-1-51 for...
Supramolecule | Name: M and E from Murray Valley encephalitis virus strain MVE-1-51 form a complex that assembles into anti-parallel dimers, (M-E)2, in the T=3 icosahedral particle. type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 Details: The prM and E genes of Murray Valley encephalitis virus strain MVE-1-51 were integrated into the Binjari virus genome using the Circular Polymerase Extension Reaction |
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Source (natural) | Organism: Murray Valley encephalitis virus |
Recombinant expression | Organism: Aedes albopictus (Asian tiger mosquito) / Recombinant cell: C6/36 |
-Macromolecule #1: Envelope protein E
Macromolecule | Name: Envelope protein E / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Murray Valley encephalitis virus |
Molecular weight | Theoretical: 53.762812 KDa |
Recombinant expression | Organism: Aedes albopictus (Asian tiger mosquito) |
Sequence | String: FNCLGMSSRD FIEGASGATW VDLVLEGDSC ITIMAADKPT LDIRMMNIEA TNLALVRNYC YAATVSDVST VSNCPTTGES HNTKRADHN YLCKRGVTDR GWGNGCGLFG KGSIDTCAKF TCSNSAAGRL ILPEDIKYEV GVFVHGSTDS TSHGNYSTQI G ANQAVRFT ...String: FNCLGMSSRD FIEGASGATW VDLVLEGDSC ITIMAADKPT LDIRMMNIEA TNLALVRNYC YAATVSDVST VSNCPTTGES HNTKRADHN YLCKRGVTDR GWGNGCGLFG KGSIDTCAKF TCSNSAAGRL ILPEDIKYEV GVFVHGSTDS TSHGNYSTQI G ANQAVRFT ISPNAPAITA KMGDYGEVTV ECEPRSGLNT EAYYVMTIGT KHFLVHREWF NDLLLPWTSP ASTEWRNREI LV EFEEPHA TKQSVVALGS QEGALHQALA GAIPVEFSSS TLKLTSGHLK CRVKMEKLKL KGTTYGMCTE KFTFSKNPAD TGH GTVVLE LQYTGSDGPC KIPISSVASL NDMTPVGRMV TANPYVASST ANAKVLVEIE PPFGDSYIVV GRGDKQINHH WHKE GSSIG KAFSTTLKGA QRLAALGDTA WDFGSVGGVF NSIGKAVHQV FGGAFRTLFG GMSWISQGLL GALLLWMGVN ARDKS IALA FLATGGVLLF LATNVHA |
-Macromolecule #2: Matrix protein M
Macromolecule | Name: Matrix protein M / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Murray Valley encephalitis virus |
Molecular weight | Theoretical: 8.272573 KDa |
Recombinant expression | Organism: Aedes albopictus (Asian tiger mosquito) |
Sequence | String: SITVQTHGES TLVNKKDAWL DSTKATRYLT KTENWIIRNP GYALVAVVLG WMLGSNTGQK VIFTVLLLLV APAYS |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 3 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 0 second wait time 2 second blot time -10 blot force 1 second drain time. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 2.0 µm / Calibrated defocus min: 0.6 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-25 / Number grids imaged: 1 / Number real images: 2829 / Average exposure time: 12.5 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |