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- EMDB-18522: Conserved Structures and Dynamics in 5-Proximal Regions of Betaco... -
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Open data
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Basic information
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Title | Conserved Structures and Dynamics in 5-Proximal Regions of Betacoronavirus RNA Genomes | |||||||||
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![]() | RNA structure / 5-proximal region / Coronavirus / Cryo-EM / VIRUS | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.9 Å | |||||||||
![]() | Moura TR / Purta E / Bernat A / Baulin E / Mukherjee S / Bujnicki JM | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes. Authors: Tales Rocha de Moura / Elżbieta Purta / Agata Bernat / Eva M Martín-Cuevas / Małgorzata Kurkowska / Eugene F Baulin / Sunandan Mukherjee / Jakub Nowak / Artur P Biela / Michał Rawski / ...Authors: Tales Rocha de Moura / Elżbieta Purta / Agata Bernat / Eva M Martín-Cuevas / Małgorzata Kurkowska / Eugene F Baulin / Sunandan Mukherjee / Jakub Nowak / Artur P Biela / Michał Rawski / Sebastian Glatt / Fernando Moreno-Herrero / Janusz M Bujnicki / ![]() ![]() Abstract: Betacoronaviruses are a genus within the Coronaviridae family of RNA viruses. They are capable of infecting vertebrates and causing epidemics as well as global pandemics in humans. Mitigating the ...Betacoronaviruses are a genus within the Coronaviridae family of RNA viruses. They are capable of infecting vertebrates and causing epidemics as well as global pandemics in humans. Mitigating the threat posed by Betacoronaviruses requires an understanding of their molecular diversity. The development of novel antivirals hinges on understanding the key regulatory elements within the viral RNA genomes, in particular the 5'-proximal region, which is pivotal for viral protein synthesis. Using a combination of cryo-electron microscopy, atomic force microscopy, chemical probing, and computational modeling, we determined the structures of 5'-proximal regions in RNA genomes of Betacoronaviruses from four subgenera: OC43-CoV, SARS-CoV-2, MERS-CoV, and Rousettus bat-CoV. We obtained cryo-electron microscopy maps and determined atomic-resolution models for the stem-loop-5 (SL5) region at the translation start site and found that despite low sequence similarity and variable length of the helical elements it exhibits a remarkable structural conservation. Atomic force microscopy imaging revealed a common domain organization and a dynamic arrangement of structural elements connected with flexible linkers across all four Betacoronavirus subgenera. Together, these results reveal common features of a critical regulatory region shared between different Betacoronavirus RNA genomes, which may allow targeting of these RNAs by broad-spectrum antiviral therapeutics. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 252.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.5 KB 15.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19.3 KB | Display | ![]() |
Images | ![]() | 37.4 KB | ||
Filedesc metadata | ![]() | 4.9 KB | ||
Others | ![]() ![]() | 474.8 MB 474.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qo4MC ![]() 8qo2C ![]() 8qo3C ![]() 8qo5C M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_18522_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18522_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Middle East respiratory syndrome-related coronavirus
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Middle East respiratory syndrome-related coronavirus
Supramolecule | Name: Middle East respiratory syndrome-related coronavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: in vitro transcription / NCBI-ID: 1335626 Sci species name: Middle East respiratory syndrome-related coronavirus Virus type: VIROID / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes |
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Host (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: MERS-CoV-SL5
Macromolecule | Name: MERS-CoV-SL5 / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 50.119512 KDa |
Sequence | String: UUUUUCAGUU AGAGCGUCGU GUCUCUUGUA CGUCUCGGUC ACAAUACACG GUUUCGUCCG GUGCGUGGCA AUUCGGGGCA CAUCAUGUC UUUCGUGGCU GGUGUGACCG CGCAAGGUGC GCGCGGUACG UAUCGAGCAG CGCUCAACUC UGAAAAA GENBANK: GENBANK: NC_019843.3 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.9 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
Details: 20 mM HEPES pH 7.5, 50 mM KCl, 50 mM NaCl | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 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 |