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Yorodumi- EMDB-17946: Tick-borne encephalitis virus (strain Neudoerfl) immature particle -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17946 | |||||||||
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Title | Tick-borne encephalitis virus (strain Neudoerfl) immature particle | |||||||||
Map data | immature particle of tick-borne encephalitis virus (strain Neudorfl) | |||||||||
Sample |
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Keywords | immature particle / tick-borne / flavivirus / whole particle / VIRUS | |||||||||
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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity ...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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / 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 / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Tick-borne encephalitis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.02 Å | |||||||||
Authors | Fuzik T / Plevka P / Smerdova L / Novacek J | |||||||||
Funding support | Czech Republic, 2 items
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Citation | Journal: Sci Adv / Year: 2024 Title: The structure of immature tick-borne encephalitis virus supports the collapse model of flavivirus maturation. Authors: Maria Anastasina / Tibor Füzik / Aušra Domanska / Lauri Ilmari Aurelius Pulkkinen / Lenka Šmerdová / Petra Pokorná Formanová / Petra Straková / Jiří Nováček / Daniel Růžek / ...Authors: Maria Anastasina / Tibor Füzik / Aušra Domanska / Lauri Ilmari Aurelius Pulkkinen / Lenka Šmerdová / Petra Pokorná Formanová / Petra Straková / Jiří Nováček / Daniel Růžek / Pavel Plevka / Sarah Jane Butcher / Abstract: We present structures of three immature tick-borne encephalitis virus (TBEV) isolates. Our atomic models of the major viral components, the E and prM proteins, indicate that the pr domains of prM ...We present structures of three immature tick-borne encephalitis virus (TBEV) isolates. Our atomic models of the major viral components, the E and prM proteins, indicate that the pr domains of prM have a critical role in holding the heterohexameric prM3E3 spikes in a metastable conformation. Destabilization of the prM furin-sensitive loop at acidic pH facilitates its processing. The prM topology and domain assignment in TBEV is similar to the mosquito-borne Binjari virus, but is in contrast to other immature flavivirus models. These results support that prM cleavage, the collapse of E protein ectodomains onto the virion surface, the large movement of the membrane domains of both E and M, and the release of the pr fragment from the particle render the virus mature and infectious. Our work favors the collapse model of flavivirus maturation warranting further studies of immature flaviviruses to determine the sequence of events and mechanistic details driving flavivirus maturation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17946.map.gz | 110.4 MB | EMDB map data format | |
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Header (meta data) | emd-17946-v30.xml emd-17946.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17946_fsc.xml | 18.2 KB | Display | FSC data file |
Images | emd_17946.png | 232.6 KB | ||
Masks | emd_17946_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-17946.cif.gz | 5.7 KB | ||
Others | emd_17946_half_map_1.map.gz emd_17946_half_map_2.map.gz | 407.7 MB 407.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17946 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17946 | HTTPS FTP |
-Validation report
Summary document | emd_17946_validation.pdf.gz | 953.8 KB | Display | EMDB validaton report |
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Full document | emd_17946_full_validation.pdf.gz | 953.3 KB | Display | |
Data in XML | emd_17946_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | emd_17946_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17946 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17946 | HTTPS FTP |
-Related structure data
Related structure data | 8ppqC 8puvC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17946.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | immature particle of tick-borne encephalitis virus (strain Neudorfl) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.563 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17946_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 2 of the gold standard reconstruction...
File | emd_17946_half_map_1.map | ||||||||||||
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Annotation | half map 2 of the gold standard reconstruction of immature particle of tick-borne encephalitis virus (strain Neudorfl) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1 of the gold standard reconstruction...
File | emd_17946_half_map_2.map | ||||||||||||
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Annotation | half map 1 of the gold standard reconstruction of immature particle of tick-borne encephalitis virus (strain Neudorfl) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tick-borne encephalitis virus
Entire | Name: Tick-borne encephalitis virus |
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Components |
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-Supramolecule #1: Tick-borne encephalitis virus
Supramolecule | Name: Tick-borne encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: Immature particles produced using tissue cell cultures NCBI-ID: 11084 / Sci species name: Tick-borne encephalitis virus / Sci species strain: Neudoerfl / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Virus shell | Shell ID: 1 / Name: immature particle / Diameter: 600.0 Å |
-Macromolecule #1: Envelope protein E
Macromolecule | Name: Envelope protein E / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Tick-borne encephalitis virus / Strain: Neudoerfl |
Sequence | String: SRCTHLENRD FVTGTQGTTR VTLVLELGGC VTITAEGKPS MDVWLDAIYQ ENPAKTREYC LHAKLSDTKV AARCPTMGPA TLAEEHQGGT VCKRDQSDRG WGNHCGLFGK GSIVACVKAA CEAKKKATGH VYDANKIVYT VKVEPHTGDY VAANETHSGR KTASFTISSE ...String: SRCTHLENRD FVTGTQGTTR VTLVLELGGC VTITAEGKPS MDVWLDAIYQ ENPAKTREYC LHAKLSDTKV AARCPTMGPA TLAEEHQGGT VCKRDQSDRG WGNHCGLFGK GSIVACVKAA CEAKKKATGH VYDANKIVYT VKVEPHTGDY VAANETHSGR KTASFTISSE KTILTMGEYG DVSLLCRVAS GVDLAQTVIL ELDKTVEHLP TAWQVHRDWF NDLALPWKHE GAQNWNNAER LVEFGAPHAV KMDVYNLGDQ TGVLLKALAG VPVAHIEGTK YHLKSGHVTC EVGLEKLKMK GLTYTMCDKT KFTWKRAPTD SGHDTVVMEV TFSGTKPCRI PVRAVAHGSP DVNVAMLITP NPTIENNGGG FIEMQLPPGD NIIYVGELSH QWFQKGSSIG RVFQKTKKGI ERLTVIGEHA WDFGSAGGFL SSIGKAVHTV LGGAFNSIFG GVGFLPKLLL GVALAWLGLN MRNPTMSMSF LLAGGLVLAM TLGVGA UniProtKB: Genome polyprotein |
-Macromolecule #2: Protein prM
Macromolecule | Name: Protein prM / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Tick-borne encephalitis virus / Strain: Neudoerfl |
Sequence | String: TVRKERDGST VIRAEGKDAA TQVRVENGTC VILATDMGSW CDDSLSYECV TIDQGEEPVD VDCFCRNVDG VYLEYGRCGK QEGSRTRRSV LIPSHAQGEL TGRGHKWLEG DSLRTHLTRV EGWVWKNKLL ALAMVTVVWL TLESVVTRVA VLVVLLCLAP VYA UniProtKB: Genome polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | ||||||||||||
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Buffer | pH: 8.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 280 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | purified immature particles of Tick-borne encephalitis virus |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 11246 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2 Details: collected in movie mode total 40 fractions per micrograph |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |