+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17808 | ||||||||||||||||||||||||
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Title | Tick-borne encephalitis virus Kuutsalo-14 prM3E3 trimer | ||||||||||||||||||||||||
Map data | Locally-sharpened map | ||||||||||||||||||||||||
Sample |
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Keywords | Complex / Spike / Fusion protein / Glycosylation / Transmembrane protein / Maturation / Virus / Trimer / Hexamer / Dimer | ||||||||||||||||||||||||
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 / 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 / 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 / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / 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 / virion membrane / structural molecule activity / 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: 3.9 Å | ||||||||||||||||||||||||
Authors | Anastasina M / Domanska A / Pulkkinen LIA / Butcher SJ | ||||||||||||||||||||||||
Funding support | Sweden, Finland, European Union, 7 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_17808.map.gz | 1.4 MB | EMDB map data format | |
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Header (meta data) | emd-17808-v30.xml emd-17808.xml | 21.5 KB 21.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17808_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_17808.png | 119.7 KB | ||
Filedesc metadata | emd-17808.cif.gz | 6.7 KB | ||
Others | emd_17808_additional_1.map.gz emd_17808_half_map_1.map.gz emd_17808_half_map_2.map.gz | 2.1 MB 47.3 MB 47.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17808 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17808 | HTTPS FTP |
-Validation report
Summary document | emd_17808_validation.pdf.gz | 705.1 KB | Display | EMDB validaton report |
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Full document | emd_17808_full_validation.pdf.gz | 704.7 KB | Display | |
Data in XML | emd_17808_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_17808_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17808 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17808 | HTTPS FTP |
-Related structure data
Related structure data | 8ppqMC 8puvC M: atomic model generated by this map 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_17808.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Locally-sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.075 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Globally-sharpened map
File | emd_17808_additional_1.map | ||||||||||||
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Annotation | Globally-sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_17808_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_17808_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
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: #1-#2 Details: Immature virions produced by infected cells treated with ammonium chloride to prevent virus maturation. NCBI-ID: 11084 / Sci species name: Tick-borne encephalitis virus / Sci species strain: Kuutsalo-14 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Ixodes ricinus (castor bean tick) |
-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: Tick-borne encephalitis virus |
Molecular weight | Theoretical: 53.55827 KDa |
Sequence | String: SRCTHLENRD FVTGTQGTTR VTLVLELGGC VTITAEGKPS MDVWLDAIYQ ENPAKTREYC LHAKLSDTKV AARCPTMGPA TLAEEHQGG TVCKRDQSDR GWGNHCGLFG KGSIVACVKA ACEAKKKATG HVYDANKIVY TVKVEPHTGD YVAANETHSG R KTASFTVS ...String: SRCTHLENRD FVTGTQGTTR VTLVLELGGC VTITAEGKPS MDVWLDAIYQ ENPAKTREYC LHAKLSDTKV AARCPTMGPA TLAEEHQGG TVCKRDQSDR GWGNHCGLFG KGSIVACVKA ACEAKKKATG HVYDANKIVY TVKVEPHTGD YVAANETHSG R KTASFTVS SEKTILTMGE YGDVSLLCRV ASGVDLAQTV ILELDKTVEH LPTAWQVHRD WFNDLALPWK HEGAQNWNNA ER LVEFGAP HAVKMDVYNL GDQTGVLLKA LAGVPVAHIE GTKYHLKSGH VTCEVGLEKL KMKGLTYTMC DKTKFTWKRA PTD SGHDTV VMEVTFSGTK PCRIPVRAVA HGSPDVNVAM LITPNPTIEN NGGGFIEMQL PPGDNIIYVG ELSHQWFQKG SSIG RVFQK TKKGIERLTV IGEHAWDFGS AGGFLSSIGK AVHTVLGGAF NSIFGGVGFL PKLLLGVALA WLGLNMRNPT MSMSF LLAG GLVLAMTLGV GA UniProtKB: Genome polyprotein |
-Macromolecule #2: Protein prM
Macromolecule | Name: Protein prM / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Tick-borne encephalitis virus |
Molecular weight | Theoretical: 18.07667 KDa |
Sequence | String: TVRKERDGST VIRAEGKDAA TQVRVENGTC VILATDMGSW CDDSLSYECV TIDQGEEPVD VDCFCRNVDG VYLEYGRCGK QEGSRTRRS VLIPSHAQGE LTGRGHKWLE GDSLRTHLTR VEGWVWKNKL LALAMVTVVW LTLESVVTRV AVLVVLLCLA P VYA UniProtKB: Genome polyprotein |
-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
Buffer | pH: 8.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Number real images: 40138 / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: ITasser / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-8ppq: |