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Yorodumi- EMDB-22296: The 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22296 | ||||||||||||||||||||||||
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Title | The 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome | ||||||||||||||||||||||||
Map data | 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome | ||||||||||||||||||||||||
Sample |
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Keywords | Frameshift Stimulation Element / SARS-CoV-2 / COVID-19 / RNA | ||||||||||||||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.9 Å | ||||||||||||||||||||||||
Authors | Zhang K / Zheludev I | ||||||||||||||||||||||||
Funding support | United States, 7 items
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Citation | Journal: bioRxiv / Year: 2020 Title: Cryo-electron Microscopy and Exploratory Antisense Targeting of the 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome. Authors: Kaiming Zhang / Ivan N Zheludev / Rachel J Hagey / Marie Teng-Pei Wu / Raphael Haslecker / Yixuan J Hou / Rachael Kretsch / Grigore D Pintilie / Ramya Rangan / Wipapat Kladwang / Shanshan Li ...Authors: Kaiming Zhang / Ivan N Zheludev / Rachel J Hagey / Marie Teng-Pei Wu / Raphael Haslecker / Yixuan J Hou / Rachael Kretsch / Grigore D Pintilie / Ramya Rangan / Wipapat Kladwang / Shanshan Li / Edward A Pham / Claire Bernardin-Souibgui / Ralph S Baric / Timothy P Sheahan / Victoria D Souza / Jeffrey S Glenn / Wah Chiu / Rhiju Das Abstract: Drug discovery campaigns against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are beginning to target the viral RNA genome . The frameshift stimulation element (FSE) of the SARS-CoV- ...Drug discovery campaigns against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are beginning to target the viral RNA genome . The frameshift stimulation element (FSE) of the SARS-CoV-2 genome is required for balanced expression of essential viral proteins and is highly conserved, making it a potential candidate for antiviral targeting by small molecules and oligonucleotides . To aid global efforts focusing on SARS-CoV-2 frameshifting, we report exploratory results from frameshifting and cellular replication experiments with locked nucleic acid (LNA) antisense oligonucleotides (ASOs), which support the FSE as a therapeutic target but highlight difficulties in achieving strong inactivation. To understand current limitations, we applied cryogenic electron microscopy (cryo-EM) and the Ribosolve pipeline to determine a three-dimensional structure of the SARS-CoV-2 FSE, validated through an RNA nanostructure tagging method. This is the smallest macromolecule (88 nt; 28 kDa) resolved by single-particle cryo-EM at subnanometer resolution to date. The tertiary structure model, defined to an estimated accuracy of 5.9 Å, presents a topologically complex fold in which the 5' end threads through a ring formed inside a three-stem pseudoknot. Our results suggest an updated model for SARS-CoV-2 frameshifting as well as binding sites that may be targeted by next generation ASOs and small molecules. | ||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22296.map.gz | 16.6 MB | EMDB map data format | |
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Header (meta data) | emd-22296-v30.xml emd-22296.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
Images | emd_22296.png | 70.6 KB | ||
Filedesc metadata | emd-22296.cif.gz | 4.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22296 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22296 | HTTPS FTP |
-Validation report
Summary document | emd_22296_validation.pdf.gz | 381.7 KB | Display | EMDB validaton report |
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Full document | emd_22296_full_validation.pdf.gz | 381.3 KB | Display | |
Data in XML | emd_22296_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | emd_22296_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22296 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22296 | HTTPS FTP |
-Related structure data
Related structure data | 6xrzMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22296.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome
Entire | Name: 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome |
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Components |
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-Supramolecule #1: 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome
Supramolecule | Name: 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 28 KDa |
-Macromolecule #1: Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome
Macromolecule | Name: Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 28.28566 KDa |
Sequence | String: GUUUUUAAAC GGGUUUGCGG UGUAAGUGCA GCCCGUCUUA CACCGUGCGG CACAGGCACU AGUACUGAUG UCGUAUACAG GGCUUUUG GENBANK: GENBANK: MT655131.1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 10222 / Average exposure time: 6.0 sec. / Average electron dose: 8.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
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
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.2) / Number images used: 109137 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |