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- EMDB-60249: Cryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state) -

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Basic information

Entry
Database: EMDB / ID: EMD-60249
TitleCryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state)
Map dataCryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state)
Sample
  • Complex: Cryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state)
    • Protein or peptide: tyrosine--tRNA ligase
    • RNA: RNA (169-MER)
KeywordsBrome osaic Virus / tRNA-like structure / aminoacylation / tyrosyl-tRNA synthetase / LIGASE/RNA / LIGASE-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 (French bean) / Brome mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsZhang K / Li S / Yang W
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into dynamics of the BMV TLS aminoacylation.
Authors: Wen Yang / Ran Yi / Jing Yao / Yongxiang Gao / Shanshan Li / Qingguo Gong / Kaiming Zhang /
Abstract: Brome Mosaic Virus (BMV) utilizes a tRNA-like structure (TLS) within its 3' untranslated region to mimic host tRNA functions, aiding aminoacylation and viral replication. This study explores the ...Brome Mosaic Virus (BMV) utilizes a tRNA-like structure (TLS) within its 3' untranslated region to mimic host tRNA functions, aiding aminoacylation and viral replication. This study explores the structural dynamics of BMV TLS interacting with tyrosyl-tRNA synthetase (TyrRS) during aminoacylation. Using cryo-EM, we capture multiple states of the TLS-TyrRS complex, including unbound TLS, pre-1a, post-1a, and catalysis states, with resolutions of 4.6 Å, 3.5 Å, 3.7 Å, and 3.85 Å, respectively. These structural comparisons indicate dynamic changes in both TLS and TyrRS. Upon binding, TLS undergoes dynamic rearrangements, particularly with helices B3 and E pivoting, mediated by the unpaired A36 residue, ensuring effective recognition by TyrRS. The dynamic changes also include a more compact arrangement in the catalytic center of TyrRS and the insertion of 3' CCA end into the enzyme's active site, facilitating two-steps aminoacylation. Enzymatic assays further demonstrated the functional importance of TLS-TyrRS interactions, with mutations in key residues significantly impacting aminoacylation efficiency. Furthermore, Electrophoretic Mobility Shift Assay (EMSA) demonstrated that BMV TLS binds elongation factors EF1α and EF2, suggesting a multifaceted strategy to exploit host translational machinery. These findings not only enhance our knowledge of virus-host interactions but also offer potential targets for antiviral drug development.
History
DepositionMay 23, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60249.png

Downloads & links

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Map

FileDownload / File: emd_60249.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.092655964 - 0.27753988
Average (Standard dev.)-0.00025089007 (±0.009249062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 275.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state)

Fileemd_60249_additional_1.map
AnnotationCryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state)

Fileemd_60249_half_map_1.map
AnnotationCryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state)

Fileemd_60249_half_map_2.map
AnnotationCryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state)

EntireName: Cryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state)
Components
  • Complex: Cryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state)
    • Protein or peptide: tyrosine--tRNA ligase
    • RNA: RNA (169-MER)

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Supramolecule #1: Cryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state)

SupramoleculeName: Cryo-EM structure of BMV TLS-TyrRS-YMP(post-1a state) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Phaseolus vulgaris (French bean)
Molecular weightTheoretical: 120 KDa

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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 (French bean)
Molecular weightTheoretical: 43.179648 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw_1 (virus)
SequenceString: MEQAPSEALQ SLSVSDSQIP QSSNSTPQLS PEEKFKIVRS VGEECIQEDE LLNLLTKKPE PVCYDGFEPS GRMHIAQGVM KTISVNKLT SAGCRVKIWI ADWFAKLNNK MGGDLKKIET VGRYLIEIWK AVGMDVEGGK VEFLWSSKEI NARADEYWPL V LDIAQKNN ...String:
MEQAPSEALQ SLSVSDSQIP QSSNSTPQLS PEEKFKIVRS VGEECIQEDE LLNLLTKKPE PVCYDGFEPS GRMHIAQGVM KTISVNKLT SAGCRVKIWI ADWFAKLNNK MGGDLKKIET VGRYLIEIWK AVGMDVEGGK VEFLWSSKEI NARADEYWPL V LDIAQKNN LKRIIRCSQI MGRSEQDELT AAQIFYPCMQ CADIFFLKAD ICQLGMDQRK VNVLAREYCD DIKRKNKPII LS HHMLPGL QQGQEKMSKS DPSSSVFMED EEAEVNVKIK KAYCPPKVVE GNPCLEYIKY LILPWFNEFT VERSADNGGN KTF KSYEEL IADYESGELH PADLKPALSK SLNKILEPVR EHFRKDSNAK ELLKRVKAYR VTK

UniProtKB: tyrosine--tRNA ligase

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Macromolecule #2: RNA (169-MER)

MacromoleculeName: RNA (169-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Brome mosaic virus
Molecular weightTheoretical: 54.354141 KDa
SequenceString:
CGUGGUUGAC ACGCAGACCU CUUACAAGAG UGUCUAGGUG CCUUUGAGAG UUACUCUUUG CUCUCUUCGG AAGAACCCUU AGGGGUUCG UGCAUGGGCU UGCAUAGCAA GUCUUAGAAU GCGGGUACCG UACAGUGUUG AAAAACACUG UAAAUCUCUA A AAGAGACC A

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

Concentration1 mg/mL
BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4849335
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 325881
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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