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- EMDB-43137: SARS-CoV-2 Frameshift Stimulatory Element with Upstream Multibran... -
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Open data
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Basic information
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Title | SARS-CoV-2 Frameshift Stimulatory Element with Upstream Multibranch Loop | |||||||||
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![]() | RNA / Coronavirus / SARS-CoV-2 / Programmed -1 Ribosomal Frameshifting / -1 PRF / Frameshift Stimulatory Element / FSE / Attenuator Hairpin | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.1 Å | |||||||||
![]() | Peterson JM / Becker ST / O'Leary CA / Juneja P / Yang Y / Moss WN | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 15.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.9 KB 17.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.7 KB | Display | ![]() |
Images | ![]() | 132.1 KB | ||
Masks | ![]() | 30.5 MB | ![]() | |
Filedesc metadata | ![]() | 5 KB | ||
Others | ![]() ![]() ![]() | 28.6 MB 28.3 MB 28.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 892.2 KB | Display | ![]() |
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Full document | ![]() | 891.7 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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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
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Density Histograms |
-Additional map: #1
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Density Histograms |
-Half map: #1
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Density Histograms |
-Half map: #2
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Density Histograms |
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Sample components
-Entire : Severe acute respiratory syndrome coronavirus
Entire | Name: ![]() |
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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: ![]() |
-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: ![]() ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-8vci: |