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- PDB-7sc6: tRNA-like Structure from Brome Mosaic Virus Bound to Tyrosyl-tRNA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sc6 | ||||||||||||
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Title | tRNA-like Structure from Brome Mosaic Virus Bound to Tyrosyl-tRNA Synthetase from Phaseolus vulgaris. Conformation: Bound State 1. | ||||||||||||
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![]() | RNA BINDING PROTEIN/RNA / tRNA-synthetase / Viral RNA / 3' UTR / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||||||||
Function / homology | ![]() tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.51 Å | ||||||||||||
![]() | Kieft, J.S. / Bonilla, S.L. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 358 KB | Display | ![]() |
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PDB format | ![]() | 287.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 46.6 KB | Display | |
Data in CIF | ![]() | 68.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 25023MC ![]() 7samC ![]() 7scqC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 45482.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: RNA chain | | Mass: 55044.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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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 |
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Sample preparation
Component | Name: RNA-protein complex: tyrosyl-tRNA synthetase from Phaseolus vulgaris bound to tRNA-like structure from brome mosaic virus RNA 3. Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / 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: 277 K / Details: Blot for 2.5 seconds before plunging. |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: cryoSPARC / Category: image acquisition | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129643 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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