+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23147 | |||||||||
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Title | Binjari virus (BinJV) | |||||||||
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 / membrane => GO:0016020 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / membrane => GO:0016020 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / extracellular region / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Binjari virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Hardy JM / Venugopal HV / Newton ND / Watterson D / Coulibaly FJ | |||||||||
Funding support | Australia, 1 items
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Citation | Journal: Sci Adv / Year: 2021 Title: The structure of an infectious immature flavivirus redefines viral architecture and maturation. Authors: Natalee D Newton / Joshua M Hardy / Naphak Modhiran / Leon E Hugo / Alberto A Amarilla / Summa Bibby / Hariprasad Venugopal / Jessica J Harrison / Renee J Traves / Roy A Hall / Jody Hobson- ...Authors: Natalee D Newton / Joshua M Hardy / Naphak Modhiran / Leon E Hugo / Alberto A Amarilla / Summa Bibby / Hariprasad Venugopal / Jessica J Harrison / Renee J Traves / Roy A Hall / Jody Hobson-Peters / Fasséli Coulibaly / Daniel Watterson / Abstract: Flaviviruses are the cause of severe human diseases transmitted by mosquitoes and ticks. These viruses use a potent fusion machinery to enter target cells that needs to be restrained during viral ...Flaviviruses are the cause of severe human diseases transmitted by mosquitoes and ticks. These viruses use a potent fusion machinery to enter target cells that needs to be restrained during viral assembly and egress. A molecular chaperone, premembrane (prM) maintains the virus particles in an immature, fusion-incompetent state until they exit the cell. Taking advantage of an insect virus that produces particles that are both immature and infectious, we determined the structure of the first immature flavivirus with a complete spike by cryo-electron microscopy. Unexpectedly, the prM chaperone forms a supporting pillar that maintains the immature spike in an asymmetric and upright state, primed for large rearrangements upon acidification. The collapse of the spike along a path defined by the prM chaperone is required, and its inhibition by a multivalent immunoglobulin M blocks infection. The revised architecture and collapse model are likely to be conserved across flaviviruses. | |||||||||
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_23147.map.gz | 270 MB | EMDB map data format | |
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Header (meta data) | emd-23147-v30.xml emd-23147.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
Images | emd_23147.png | 302.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23147 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23147 | HTTPS FTP |
-Validation report
Summary document | emd_23147_validation.pdf.gz | 371.7 KB | Display | EMDB validaton report |
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Full document | emd_23147_full_validation.pdf.gz | 371.3 KB | Display | |
Data in XML | emd_23147_validation.xml.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23147 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23147 | HTTPS FTP |
-Related structure data
Related structure data | 7l30MC 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_23147.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Local-resolution filtered map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 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 : 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: all Details: M and E from Binjari virus form a complex that assembles into anti-parallel dimers, (M-E)2, in the T=3 icosahedral particle. 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: 22 MDa |
Virus shell | Shell ID: 1 / Diameter: 470.0 Å / T number (triangulation number): 3 |
-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: Binjari virus |
Molecular weight | Theoretical: 53.495086 KDa |
Recombinant expression | Organism: Aedes albopictus (Asian tiger mosquito) |
Sequence | String: NQCLDVQSRD FVQGVSGGTW VDVVLDHDNC ITIVADGKPS FDIRLSKMSM SKFAEYKRYC LQATMSDVTS IVACPGAGDA HNDKSKNHE YICKAVNNDR GWGNGCVLFG KGSMETCGKF ECKKKMAGKL VARENVESVV TVHVHGASAT DTKGVDTAST A KATITPKA ...String: NQCLDVQSRD FVQGVSGGTW VDVVLDHDNC ITIVADGKPS FDIRLSKMSM SKFAEYKRYC LQATMSDVTS IVACPGAGDA HNDKSKNHE YICKAVNNDR GWGNGCVLFG KGSMETCGKF ECKKKMAGKL VARENVESVV TVHVHGASAT DTKGVDTAST A KATITPKA SVATLNLNDF GSLEVDCSTD VGMDFGEIVV ADMSGKWWIV NKDWFNELAL PWSTASTTAE VWQARDRLVE FG WPHAAKQ NIYDIGDQEG AVTAAIAQAP MAKWESDKVE LISGILKCKV KLGNLKLRGV TYSMCAQTFT TETRPADTGH GTV AFKVKY VGTDVPCRVP LHIIDSDGGV AAGRVITAHP FVMKQNDYII LEVEPPFGDS KIEIGTGTTK LVEAWHRKGS SIGN AFTAT YKGITKLTVL GEHAWDFNSL GGFGASLGKA VHTLFGGVFR VMFGGMGWLT KIFVGAVLVW LGLGAHDKTI ATTMI LVGS ILMYMAVTVG ALS |
-Macromolecule #2: prM protein
Macromolecule | Name: prM protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Binjari virus |
Molecular weight | Theoretical: 18.946809 KDa |
Recombinant expression | Organism: Aedes albopictus (Asian tiger mosquito) |
Sequence | String: ATLRTVGDLT WLNVSTTDVG KWIRVENRHG KGECFVTATD VGTWCSDSVG YECPQIAPAY DPEDLDCYCR NTSTYVTYGR CKNGRSGRS RSKRAITIAP HGEAGLRVGS TKHWTSRATP QRYLMRVEKW VLRHPLPALV LVVLGWMMGR SHGQRAMYIV L MLLVAPSY G |
-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 2.5 second blot time -4 blot force 1 second drain time. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 6226 / Average exposure time: 12.8 sec. / Average electron dose: 43.2768 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 4.3 µm / Calibrated defocus min: 0.1 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |