Database: EMDB / ID: EMD-34016
|Title||Lloviu cuevavirus nucleoprotein-RNA complex|
|Function / homology||Ebola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / viral nucleocapsid / Nucleoprotein|
Function and homology information
|Biological species||Lloviu cuevavirus (unknown) / synthetic construct (unknown)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.0356 Å|
|Authors||Hu SF / Fujita-Fujiharu Y / Sugita Y / Wendt L / Muramoto Y / Nakano M / Hoenen T / Noda T|
|Funding support|| Japan, 6 items |
|Citation||Journal: PNAS Nexus / Year: 2023|
Title: Cryoelectron microscopic structure of the nucleoprotein-RNA complex of the European filovirus, Lloviu virus.
Authors: Shangfan Hu / Yoko Fujita-Fujiharu / Yukihiko Sugita / Lisa Wendt / Yukiko Muramoto / Masahiro Nakano / Thomas Hoenen / Takeshi Noda /
Abstract: Lloviu virus (LLOV) is a novel filovirus detected in Schreiber's bats in Europe. The isolation of the infectious LLOV from bats has raised public health concerns. However, the virological and ...Lloviu virus (LLOV) is a novel filovirus detected in Schreiber's bats in Europe. The isolation of the infectious LLOV from bats has raised public health concerns. However, the virological and molecular characteristics of LLOV remain largely unknown. The nucleoprotein (NP) of LLOV encapsidates the viral genomic RNA to form a helical NP-RNA complex, which acts as a scaffold for nucleocapsid formation and de novo viral RNA synthesis. In this study, using single-particle cryoelectron microscopy, we determined two structures of the LLOV NP-RNA helical complex, comprising a full-length and a C-terminally truncated NP. The two helical structures were identical, demonstrating that the N-terminal region determines the helical arrangement of the NP. The LLOV NP-RNA protomers displayed a structure similar to that in the Ebola and Marburg virus, but the spatial arrangements in the helix differed. Structure-based mutational analysis identified amino acids involved in the helical assembly and viral RNA synthesis. These structures advance our understanding of the filovirus nucleocapsid formation and provide a structural basis for the development of antifiloviral therapeutics.
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|Map data||emd_34016.map.gz||228.8 MB||EMDB map data format|
|Header (meta data)||emd-34016-v30.xml|
|FSC (resolution estimation)||emd_34016_fsc.xml||14.1 KB||Display||FSC data file|
|Summary document||emd_34016_validation.pdf.gz||1.1 MB||Display||EMDB validaton report|
|Full document||emd_34016_full_validation.pdf.gz||1.1 MB||Display|
|Data in XML||emd_34016_validation.xml.gz||21.7 KB||Display|
|Data in CIF||emd_34016_validation.cif.gz||28.4 KB||Display|
-Related structure data
|Related structure data|
M: atomic model generated by this map
C: citing same article (ref.)
|Similar structure data|
Similarity search - Function & homologyF&H Search
Similarity search - FunctionF&H Search
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|EMDB pages||EMDB (EBI/PDBe) / EMDataResource|
|Related items in Molecule of the Month|
|File||Download / File: emd_34016.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.13 Å|
|Symmetry||Space group: 1|
-Half map: #2
|Projections & Slices|
-Half map: #1
|Projections & Slices|
-Entire : Lloviu cuevavirus nucleoprotein RNA complex
|Entire||Name: Lloviu cuevavirus nucleoprotein RNA complex|
-Supramolecule #1: Lloviu cuevavirus nucleoprotein RNA complex
|Supramolecule||Name: Lloviu cuevavirus nucleoprotein RNA complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all|
|Source (natural)||Organism: Lloviu cuevavirus (unknown)|
-Macromolecule #1: Nucleoprotein
|Macromolecule||Name: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO|
|Source (natural)||Organism: Lloviu cuevavirus (unknown) / Strain: isolate Bat/Spain/Asturias-Bat86/2003|
|Molecular weight||Theoretical: 84.553094 KDa|
|Recombinant expression||Organism: Homo sapiens (human)|
-Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
|Macromolecule||Name: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') / type: rna / ID: 2 / Number of copies: 1|
|Source (natural)||Organism: synthetic construct (unknown)|
|Molecular weight||Theoretical: 1.792037 KDa|
|Processing||single particle reconstruction|
|Aggregation state||helical array|
|Buffer||pH: 8 |
|Grid||Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR|
|Vitrification||Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV|
Details: Apply 1.25 micro litters of sample from each side of the grid and blot for 7 seconds before plugging.
|Microscope||FEI TITAN KRIOS|
|Electron beam||Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN|
|Electron optics||C2 aperture diameter: 50.0 µm / Calibrated magnification: 59000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000|
|Specialist optics||Spherical aberration corrector: Microscope was modified with a Cs corrector with two hexapole elements|
|Sample stage||Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN|
|Image recording||Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3122 / Average electron dose: 40.0 e/Å2|
Model: Titan Krios / Image courtesy: FEI Company
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