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- EMDB-25041: tRNA-like Structure from Brome Mosaic Virus Bound to Tyrosyl-tRNA... -

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Basic information

Entry
Database: EMDB / ID: EMD-25041
TitletRNA-like Structure from Brome Mosaic Virus Bound to Tyrosyl-tRNA Synthetase from Phaseolus vulgaris. Conformation: Bound State 2.
Map dataCryo-EM map of cytoplasmic tyrosyl-tRNA synthetase from Phaseolus vulgaris bound to tRNA-like structure from brome mosaic virus RNA 3. Two conformations were observed. This map is for "bound state 2".
Sample
  • Complex: RNA-protein complex: tyrosyl-tRNA synthetase from Phaseolus vulgaris bound to tRNA-like structure from brome mosaic virus RNA 3.
    • Protein or peptide: Tyrosine--tRNA ligase
    • RNA: tRNA-like structure from brome mosaic virus RNA 3.
KeywordstRNA-synthetase / RNA-protein complex / Viral RNA / 3' UTR / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, archaeal/eukaryotic-type / : / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
tyrosine--tRNA ligase
Similarity search - Component
Biological speciesPhaseolus vulgaris (common bean) / Brome mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsKieft JS / Bonilla SL
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118070 United States
National Science Foundation (NSF, United States)F32GM139385 United States
Howard Hughes Medical Institute (HHMI)Hanna H. Gray Fellowship United States
CitationJournal: 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
DepositionSep 28, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0318
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0318
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7scq
  • Surface level: 0.0318
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25041.png

Downloads & links

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Map

FileDownload / File: emd_25041.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of cytoplasmic tyrosyl-tRNA synthetase from Phaseolus vulgaris bound to tRNA-like structure from brome mosaic virus RNA 3. Two conformations were observed. This map is for "bound state 2".
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 432 pix.
= 358.56 Å		0.83 Å/pix.
x 432 pix.
= 358.56 Å		0.83 Å/pix.
x 432 pix.
= 358.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0318 / Movie #1: 0.0318
Minimum - Maximum-0.08998322 - 0.31627062
Average (Standard dev.)-0.00009491328 (±0.0044187824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 358.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z358.560358.560358.560
α/β/γ90.00090.00090.000
start NX/NY/NZ-140-140-140
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0900.316-0.000

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Supplemental data

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Half map: Half-map A of cytoplasmic tyrosyl-tRNA synthetase from Phaseolus...

Fileemd_25041_half_map_1.map
AnnotationHalf-map A of cytoplasmic tyrosyl-tRNA synthetase from Phaseolus vulgaris bound to tRNA-like structure from brome mosaic virus RNA 3. Two conformations were observed. This map is for "bound state 2".
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B of cytoplasmic tyrosyl-tRNA synthetase from Phaseolus...

Fileemd_25041_half_map_2.map
AnnotationHalf-map B of cytoplasmic tyrosyl-tRNA synthetase from Phaseolus vulgaris bound to tRNA-like structure from brome mosaic virus RNA 3. Two conformations were observed. This map is for "bound state 2".
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNA-protein complex: tyrosyl-tRNA synthetase from Phaseolus vulga...

EntireName: RNA-protein complex: tyrosyl-tRNA synthetase from Phaseolus vulgaris bound to tRNA-like structure from brome mosaic virus RNA 3.
Components
  • Complex: RNA-protein complex: tyrosyl-tRNA synthetase from Phaseolus vulgaris bound to tRNA-like structure from brome mosaic virus RNA 3.
    • Protein or peptide: Tyrosine--tRNA ligase
    • RNA: tRNA-like structure from brome mosaic virus RNA 3.

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Supramolecule #1: RNA-protein complex: tyrosyl-tRNA synthetase from Phaseolus vulga...

SupramoleculeName: 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
Source (natural)Organism: Phaseolus vulgaris (common bean)

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Macromolecule #1: Tyrosine--tRNA ligase

MacromoleculeName: Tyrosine--tRNA ligase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: tyrosine-tRNA ligase
Source (natural)Organism: Phaseolus vulgaris (common bean)
Molecular weightTheoretical: 45.482191 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

UniProtKB: tyrosine--tRNA ligase

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Macromolecule #2: tRNA-like structure from brome mosaic virus RNA 3.

MacromoleculeName: tRNA-like structure from brome mosaic virus RNA 3. / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Brome mosaic virus
Molecular weightTheoretical: 55.044559 KDa
SequenceString:
GGCGUGGUUG ACACGCAGAC CUCUUACAAG AGUGUCUAGG UGCCUUUGAG AGUUACUCUU UGCUCUCUUC GGAAGAACCC UUAGGGGUU CGUGCAUGGG CUUGCAUAGC AAGUCUUAGA AUGCGGGUAC CGUACAGUGU UGAAAAACAC UGUAAAUCUC U AAAAGAGA CCA

GENBANK: GENBANK: X58457.1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
GridModel: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 2.5 seconds before plunging..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 122118
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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