+Open data
-Basic information
Entry | Database: PDB / ID: 7sam | ||||||||||||
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Title | tRNA-like Structure from Brome Mosaic Virus | ||||||||||||
Components | Viral RNA | ||||||||||||
Keywords | RNA / Viral RNA / 3' UTR | ||||||||||||
Function / homology | RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||||||||
Biological species | Brome mosaic virus | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||||||||
Authors | Kieft, J.S. / Bonilla, S.L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Science / Year: 2021 Title: A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure. Authors: Steve L Bonilla / Madeline E Sherlock / Andrea MacFadden / Jeffrey S Kieft / Abstract: Viruses require multifunctional structured RNAs to hijack their host’s biochemistry, but their mechanisms can be obscured by the difficulty of solving conformationally dynamic RNA structures. Using ...Viruses require multifunctional structured RNAs to hijack their host’s biochemistry, but their mechanisms can be obscured by the difficulty of solving conformationally dynamic RNA structures. Using cryo–electron microscopy (cryo-EM), we visualized the structure of the mysterious viral transfer RNA (tRNA)–like structure (TLS) from the brome mosaic virus, which affects replication, translation, and genome encapsidation. Structures in isolation and those bound to tyrosyl-tRNA synthetase (TyrRS) show that this ~55-kilodalton purported tRNA mimic undergoes large conformational rearrangements to bind TyrRS in a form that differs substantially from that of tRNA. Our study reveals how viral RNAs can use a combination of static and dynamic RNA structures to bind host machinery through highly noncanonical interactions, and we highlight the utility of cryo-EM for visualizing small, conformationally dynamic structured RNAs. | ||||||||||||
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 | 7sam.cif.gz | 122.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sam.ent.gz | 92 KB | Display | PDB format |
PDBx/mmJSON format | 7sam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sam_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7sam_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7sam_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 7sam_validation.cif.gz | 44.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/7sam ftp://data.pdbj.org/pub/pdb/validation_reports/sa/7sam | HTTPS FTP |
-Related structure data
Related structure data | 24952MC 7sc6C 7scqC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10993 (Title: Cryo-EM micrographs of BMV TLS RNA / Data size: 6.7 TB Data #1: Aligned micrographs (with and without dose-weighting), dataset 1 [micrographs - single frame] Data #2: Aligned micrographs (with and without dose-weighting), dataset 2 [micrographs - single frame]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: RNA chain | Mass: 55044.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcribed / Source: (synth.) Brome mosaic virus |
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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: tRNA-like structure at the 3' UTR of the brome mosaic virus (BMV) genome Type: COMPLEX Details: RNA was generated by in vitro transcription of sequence-verified linear DNA template Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.05456 MDa / Experimental value: NO |
Source (natural) | Organism: Brome mosaic virus |
Buffer solution | pH: 7 / Details: Solution contained 10 mM magnesium chloride. |
Buffer component | Conc.: 50 mM / Name: NaMOPS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: This sample was monodisperse as determined by native gel electrophoresis. |
Specimen support | Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: -800 nm / Nominal defocus min: -2000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software | Name: cryoSPARC / Category: 3D reconstruction | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128226 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 103.85 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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