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- EMDB-60247: Cryo-EM structure of Unbound BMV TLS -

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Basic information

Entry
Database: EMDB / ID: EMD-60247
TitleCryo-EM structure of Unbound BMV TLS
Map data
Sample
  • Complex: Cryo-EM structure of Unbound BMV TLS
    • RNA: RNA (169-MER)
KeywordsBrome Mosaic Virus / tRNA-like structure / aminoacylation / tyrosyl-tRNA synthetase / RNA
Biological speciesBrome mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsYang W / Li S / Zhang K
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_60247.png

Downloads & links

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Map

FileDownload / File: emd_60247.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
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Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.107624605 - 0.38726148
Average (Standard dev.)0.00062144356 (±0.009167311)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_60247_additional_1.map
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Half map: #1

Fileemd_60247_half_map_1.map
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Half map: #2

Fileemd_60247_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of Unbound BMV TLS

EntireName: Cryo-EM structure of Unbound BMV TLS
Components
  • Complex: Cryo-EM structure of Unbound BMV TLS
    • RNA: RNA (169-MER)

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Supramolecule #1: Cryo-EM structure of Unbound BMV TLS

SupramoleculeName: Cryo-EM structure of Unbound BMV TLS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Brome mosaic virus
Molecular weightTheoretical: 60 KDa

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Macromolecule #1: RNA (169-MER)

MacromoleculeName: RNA (169-MER) / type: rna / ID: 1 / 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

MicroscopeFEI TITAN 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

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 224970
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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