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Yorodumi- EMDB-43137: SARS-CoV-2 Frameshift Stimulatory Element with Upstream Multibran... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43137 | |||||||||
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Title | SARS-CoV-2 Frameshift Stimulatory Element with Upstream Multibranch Loop | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RNA / Coronavirus / SARS-CoV-2 / Programmed -1 Ribosomal Frameshifting / -1 PRF / Frameshift Stimulatory Element / FSE / Attenuator Hairpin | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Severe acute respiratory syndrome coronavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.1 Å | |||||||||
Authors | Peterson JM / Becker ST / O'Leary CA / Juneja P / Yang Y / Moss WN | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Biochemistry / Year: 2024 Title: Structure of the SARS-CoV-2 Frameshift Stimulatory Element with an Upstream Multibranch Loop. Authors: Jake M Peterson / Scott T Becker / Collin A O'Leary / Puneet Juneja / Yang Yang / Walter N Moss / Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshift stimulatory element (FSE) is necessary for programmed -1 ribosomal frameshifting (-1 PRF) and optimized viral efficacy. The ...The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshift stimulatory element (FSE) is necessary for programmed -1 ribosomal frameshifting (-1 PRF) and optimized viral efficacy. The FSE has an abundance of context-dependent alternate conformations, but two of the structures most crucial to -1 PRF are an attenuator hairpin and a three-stem H-type pseudoknot structure. A crystal structure of the pseudoknot alone features three RNA stems in a helically stacked linear structure, whereas a 6.9 Å cryo-EM structure including the upstream heptameric slippery site resulted in a bend between two stems. Our previous research alluded to an extended upstream multibranch loop that includes both the attenuator hairpin and the slippery site-a conformation not previously modeled. We aim to provide further context to the SARS-CoV-2 FSE via computational and medium resolution cryo-EM approaches, by presenting a 6.1 Å cryo-EM structure featuring a linear pseudoknot structure and a dynamic upstream multibranch loop. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43137.map.gz | 15.1 MB | EMDB map data format | |
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Header (meta data) | emd-43137-v30.xml emd-43137.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43137_fsc.xml | 6.7 KB | Display | FSC data file |
Images | emd_43137.png | 132.1 KB | ||
Masks | emd_43137_msk_1.map | 30.5 MB | Mask map | |
Filedesc metadata | emd-43137.cif.gz | 5 KB | ||
Others | emd_43137_additional_1.map.gz emd_43137_half_map_1.map.gz emd_43137_half_map_2.map.gz | 28.6 MB 28.3 MB 28.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43137 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43137 | HTTPS FTP |
-Validation report
Summary document | emd_43137_validation.pdf.gz | 892.2 KB | Display | EMDB validaton report |
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Full document | emd_43137_full_validation.pdf.gz | 891.7 KB | Display | |
Data in XML | emd_43137_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | emd_43137_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43137 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43137 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_43137.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.133 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_43137_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_43137_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_43137_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_43137_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : Severe acute respiratory syndrome coronavirus
Entire | Name: Severe acute respiratory syndrome coronavirus |
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Components |
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-Supramolecule #1: Severe acute respiratory syndrome coronavirus
Supramolecule | Name: Severe acute respiratory syndrome coronavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: PCR amplified and transcribed using T7 polymerase. / NCBI-ID: 2901879 Sci species name: Severe acute respiratory syndrome coronavirus Sci species strain: Wuhan-Hu-1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) / Strain: Wuhan-Hu-1 |
-Macromolecule #1: Frameshift Stimulatory Element with Upstream Multi-branch Loop
Macromolecule | Name: Frameshift Stimulatory Element with Upstream Multi-branch Loop type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 37.90141 KDa |
Sequence | String: GGGAACCCAU GCUUCAGUCA GCUGAUGCAC AAUCGUUUUU AAACGGGUUU CCGGUGUAAG UGCAGCCCGU CUUACACCGU GCGGCACAG GCACUAGUAC UGAUGUCGUA UACAGGGCU GENBANK: GENBANK: NC_045512.2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 36000 |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-8vci: |