+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34049 | |||||||||||||||||||||
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Title | Lloviu cuevavirus nucleoprotein(1-450 residues)-RNA complex | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Keywords | nucleoprotein / VIRAL PROTEIN | |||||||||||||||||||||
Function / homology | Ebola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / viral nucleocapsid / Nucleoprotein Function and homology information | |||||||||||||||||||||
Biological species | Lloviu cuevavirus / synthetic construct (others) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||||||||
Authors | Hu SF / Fujita-Fujiharu Y / Sugita Y / Wendt L / Muramoto Y / Nakano M / Hoenen T / Noda T | |||||||||||||||||||||
Funding support | Japan, 6 items
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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. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34049.map.gz | 320.2 MB | EMDB map data format | |
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Header (meta data) | emd-34049-v30.xml emd-34049.xml | 20.7 KB 20.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34049_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_34049.png | 204.6 KB | ||
Others | emd_34049_half_map_1.map.gz emd_34049_half_map_2.map.gz | 271 MB 271 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34049 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34049 | HTTPS FTP |
-Related structure data
Related structure data | 7yr8MC 7ypwC 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_34049.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.96 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34049_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34049_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Lloviu cuevavirus nucleoprotein (1-450 residues) RNA complex
Entire | Name: Lloviu cuevavirus nucleoprotein (1-450 residues) RNA complex |
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Components |
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-Supramolecule #1: Lloviu cuevavirus nucleoprotein (1-450 residues) RNA complex
Supramolecule | Name: Lloviu cuevavirus nucleoprotein (1-450 residues) RNA complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Lloviu cuevavirus |
-Macromolecule #1: Nucleoprotein
Macromolecule | Name: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lloviu cuevavirus / Strain: isolate Bat/Spain/Asturias-Bat86/2003 |
Molecular weight | Theoretical: 43.197594 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ELHGILSLGL NVDHTIVRKK SIPLFEIGNS DQVCNWIIQI IEAGVDLQEV ADSFLTMLCV NHAYQGDPNL FLESPAAHYL KGHGIHFEI QHRDNVDHIT DLLGVGSRDK SLRKTLSALE FEPGGTTTAG MFLSFASLFL PKLVVGERAC LEKVQRQIQI H AEQGLIQY ...String: ELHGILSLGL NVDHTIVRKK SIPLFEIGNS DQVCNWIIQI IEAGVDLQEV ADSFLTMLCV NHAYQGDPNL FLESPAAHYL KGHGIHFEI QHRDNVDHIT DLLGVGSRDK SLRKTLSALE FEPGGTTTAG MFLSFASLFL PKLVVGERAC LEKVQRQIQI H AEQGLIQY PTQWQSVGHM MVVFRLIRVN FVLKFLLVHQ GMHMMAGHDA NDAIIANSIS QTRFSGLLIV KTVLEHILQK TE AGVQLHP LARTSKVKGE LLAFKSALEA LASHREYAPF ARLLNLSGVN NLEHGLYPQL SAIALGVATA HGSTLAGVNV SEQ YQQLRE AATEAEKQLQ QHSEMRELET LGLDEQERKI LATFHSRKNE INIQQTSSIL AIRKERLRKL T UniProtKB: Nucleoprotein |
-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 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 1.792037 KDa |
Sequence | String: UUUUUU |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | helical array |
-Sample preparation
Concentration | 0.3 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 / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.007 kPa / Details: JEC-3000FC | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Apply 1.5 micro litters of sample from each side of the grid and blot for 6 seconds before plugging. |
-Electron microscopy
Microscope | TFS GLACIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 150000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3780 / Average electron dose: 40.0 e/Å2 |