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Yorodumi- EMDB-18520: Conserved Structures and Dynamics in 5-Proximal Regions of Betaco... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18520 | |||||||||
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Title | Conserved Structures and Dynamics in 5-Proximal Regions of Betacoronavirus RNA Genomes | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RNA structure / 5-proximal region / Coronavirus / Cryo-EM / VIRUS | |||||||||
Biological species | Human coronavirus OC43 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.1 Å | |||||||||
Authors | Moura TR / Purta E / Bernat A / Baulin E / Mukherjee S / Bujnicki JM | |||||||||
Funding support | Poland, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2024 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 | emd_18520.map.gz | 250.9 MB | EMDB map data format | |
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Header (meta data) | emd-18520-v30.xml emd-18520.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18520_fsc.xml | 17.2 KB | Display | FSC data file |
Images | emd_18520.png | 36.7 KB | ||
Filedesc metadata | emd-18520.cif.gz | 5.1 KB | ||
Others | emd_18520_half_map_1.map.gz emd_18520_half_map_2.map.gz | 475.1 MB 475.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18520 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18520 | HTTPS FTP |
-Related structure data
Related structure data | 8qo2MC 8qo3C 8qo4C 8qo5C M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18520.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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_18520_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18520_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human coronavirus OC43
Entire | Name: Human coronavirus OC43 |
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Components |
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-Supramolecule #1: Human coronavirus OC43
Supramolecule | Name: Human coronavirus OC43 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: in vitro transcription / NCBI-ID: 31631 / Sci species name: Human coronavirus OC43 / Virus type: VIROID / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes |
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Host (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: OC43-CoV-SL5
Macromolecule | Name: OC43-CoV-SL5 / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: Human coronavirus OC43 |
Molecular weight | Theoretical: 71.566438 KDa |
Sequence | String: UUCUGCUGUU AACAGCUUUC AGCCAGGGAC GUGUUGUAUC CUAGGCAGUG GCCCUCCCAU AGGUCACAAU GUCGAAGAUC AACAAAUAC GGUCUCGAAC UACACUGGGC UCCAGAAUUU CCAUGGAUGU UUGAGGACGC AGAGGAGAAG UUGGACAACC C UAGUAGUU ...String: UUCUGCUGUU AACAGCUUUC AGCCAGGGAC GUGUUGUAUC CUAGGCAGUG GCCCUCCCAU AGGUCACAAU GUCGAAGAUC AACAAAUAC GGUCUCGAAC UACACUGGGC UCCAGAAUUU CCAUGGAUGU UUGAGGACGC AGAGGAGAAG UUGGACAACC C UAGUAGUU CAGAGGUGGA UAUGAUUUGC UCCACCACUG CGCAAAAGCU GGAAACAGAC GGAA GENBANK: GENBANK: OK073091.1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 | ||||||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |