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Yorodumi- EMDB-25023: tRNA-like Structure from Brome Mosaic Virus Bound to Tyrosyl-tRNA... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25023 | ||||||||||||
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Title | tRNA-like Structure from Brome Mosaic Virus Bound to Tyrosyl-tRNA Synthetase from Phaseolus vulgaris. Conformation: Bound State 1. | ||||||||||||
Map data | Cryo-EM map of tyrosyl-tRNA synthetase (TyrRS) from Phaseolus vulgaris bound to tRNA-like structure (TLS) from brome mosaic virus (BMV). Complex in 'bound state 1'. | ||||||||||||
Sample |
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Function / homology | Tyrosine-tRNA ligase, archaeal/eukaryotic-type / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / tRNA aminoacylation for protein translation / Rossmann-like alpha/beta/alpha sandwich fold / ATP binding / Tyrosine--tRNA ligase Function and homology information | ||||||||||||
Biological species | Phaseolus vulgaris (French bean) / Brome mosaic virus | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.51 Å | ||||||||||||
Authors | Kieft JS / Bonilla SL | ||||||||||||
Funding support | United States, 3 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25023.map.gz | 149.4 MB | EMDB map data format | |
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Header (meta data) | emd-25023-v30.xml emd-25023.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25023_fsc.xml | 15 KB | Display | FSC data file |
Images | emd_25023.png | 92.9 KB | ||
Others | emd_25023_additional_1.map.gz emd_25023_half_map_1.map.gz emd_25023_half_map_2.map.gz | 289.5 MB 285.6 MB 285.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25023 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25023 | HTTPS FTP |
-Related structure data
Related structure data | 7sc6MC 7samC 7scqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25023.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of tyrosyl-tRNA synthetase (TyrRS) from Phaseolus vulgaris bound to tRNA-like structure (TLS) from brome mosaic virus (BMV). Complex in 'bound state 1'. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Sharpened (B factor: 341.8) cryo-EM map of tyrosyl-tRNA...
File | emd_25023_additional_1.map | ||||||||||||
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Annotation | Sharpened (B factor: 341.8) cryo-EM map of tyrosyl-tRNA synthetase (TyrRS) from Phaseolus vulgaris bound to tRNA-like structure (TLS) from brome mosaic virus (BMV). Complex in 'bound state 1'. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map A of tyrosyl-tRNA synthetase (TyrRS) from Phaseolus...
File | emd_25023_half_map_1.map | ||||||||||||
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Annotation | Half-map A of tyrosyl-tRNA synthetase (TyrRS) from Phaseolus vulgaris bound to tRNA-like structure (TLS) from brome mosaic virus (BMV). Complex in 'bound state 1'. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map B of tyrosyl-tRNA synthetase (TyrRS) from Phaseolus...
File | emd_25023_half_map_2.map | ||||||||||||
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Annotation | Half-map B of tyrosyl-tRNA synthetase (TyrRS) from Phaseolus vulgaris bound to tRNA-like structure (TLS) from brome mosaic virus (BMV).Complex in 'bound state 1'. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RNA-protein complex: tyrosyl-tRNA synthetase from Phaseolus vulga...
Entire | Name: RNA-protein complex: tyrosyl-tRNA synthetase from Phaseolus vulgaris bound to tRNA-like structure from brome mosaic virus RNA 3. |
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Components |
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-Supramolecule #1: RNA-protein complex: tyrosyl-tRNA synthetase from Phaseolus vulga...
Supramolecule | Name: RNA-protein complex: tyrosyl-tRNA synthetase from Phaseolus vulgaris bound to tRNA-like structure from brome mosaic virus RNA 3. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Phaseolus vulgaris (French bean) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Tyrosine--tRNA ligase
Macromolecule | Name: Tyrosine--tRNA ligase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: tyrosine-tRNA ligase |
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Source (natural) | Organism: Phaseolus vulgaris (French bean) |
Molecular weight | Theoretical: 45.482191 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MMEQAPSEAL QSLSVSDSQI PQSSNSTPQL SPEEKFKIVR SVGEECIQED ELLNLLTKKP EPVCYDGFE PSGRMHIAQG VMKTISVNKL TSAGCRVKIW IADWFAKLNN KMGGDLKKIE TVGRYLIEIW KAVGMDVEGG K VEFLWSSK ...String: MGSSHHHHHH SSGLVPRGSH MMEQAPSEAL QSLSVSDSQI PQSSNSTPQL SPEEKFKIVR SVGEECIQED ELLNLLTKKP EPVCYDGFE PSGRMHIAQG VMKTISVNKL TSAGCRVKIW IADWFAKLNN KMGGDLKKIE TVGRYLIEIW KAVGMDVEGG K VEFLWSSK EINARADEYW PLVLDIAQKN NLKRIIRCSQ IMGRSEQDEL TAAQIFYPCM QCADIFFLKA DICQLGMDQR KV NVLAREY CDDIKRKNKP IILSHHMLPG LQQGQEKMSK SDPSSSVFME DEEAEVNVKI KKAYCPPKVV EGNPCLEYIK YLI LPWFNE FTVERSADNG GNKTFKSYEE LIADYESGEL HPADLKPALS KSLNKILEPV REHFRKDSNA KELLKRVKAY RVTK |
-Macromolecule #2: tRNA-like structure from brome mosaic virus RNA 3
Macromolecule | Name: tRNA-like structure from brome mosaic virus RNA 3 / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Brome mosaic virus |
Molecular weight | Theoretical: 55.044559 KDa |
Sequence | String: GGCGUGGUUG ACACGCAGAC CUCUUACAAG AGUGUCUAGG UGCCUUUGAG AGUUACUCUU UGCUCUCUUC GGAAGAACCC UUAGGGGUU CGUGCAUGGG CUUGCAUAGC AAGUCUUAGA AUGCGGGUAC CGUACAGUGU UGAAAAACAC UGUAAAUCUC U AAAAGAGA CCA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 2.5 seconds before plunging.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Specialist optics | Energy filter - Name: GIF Bioquantum |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |