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Yorodumi- PDB-6xrz: The 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xrz | ||||||||||||||||||||||||
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Title | The 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome | ||||||||||||||||||||||||
Components | Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome | ||||||||||||||||||||||||
Keywords | RNA / Frameshift Stimulation Element / SARS-CoV-2 / COVID-19 | ||||||||||||||||||||||||
Function / homology | : / RNA / RNA (> 10) Function and homology information | ||||||||||||||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.9 Å | ||||||||||||||||||||||||
Authors | Zhang, K. / Zheludev, I. / Hagey, R. / Wu, M. / Haslecker, R. / Hou, Y. / Kretsch, R. / Pintilie, G. / Rangan, R. / Kladwang, W. ...Zhang, K. / Zheludev, I. / Hagey, R. / Wu, M. / Haslecker, R. / Hou, Y. / Kretsch, R. / Pintilie, G. / Rangan, R. / Kladwang, W. / Li, S. / Pham, E. / Souibgui, C. / Baric, R. / Sheahan, T. / Souza, V. / Glenn, J. / Chiu, W. / Das, R. | ||||||||||||||||||||||||
Funding support | United States, 7items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6xrz.cif.gz | 531.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xrz.ent.gz | 459.9 KB | Display | PDB format |
PDBx/mmJSON format | 6xrz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xrz_validation.pdf.gz | 685.9 KB | Display | wwPDB validaton report |
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Full document | 6xrz_full_validation.pdf.gz | 719.3 KB | Display | |
Data in XML | 6xrz_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 6xrz_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/6xrz ftp://data.pdbj.org/pub/pdb/validation_reports/xr/6xrz | HTTPS FTP |
-Related structure data
Related structure data | 22296MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Number of models | 10 |
-Components
#1: RNA chain | Mass: 28285.660 Da / Num. of mol.: 1 / Fragment: GB residues 13434-13521 / Source method: obtained synthetically Source: (synth.) Severe acute respiratory syndrome coronavirus 2 References: GenBank: 1860584649 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.028 MDa / Experimental value: NO |
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 6 sec. / Electron dose: 8.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 10222 |
Image scans | Movie frames/image: 30 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109137 / Symmetry type: POINT |