8ZMJ | pdb_00008zmj

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural insights into dynamics of the BMV TLS aminoacylation.

Yang, W.Yi, R.Yao, J.Gao, Y.Li, S.Gong, Q.Zhang, K.

(2025) Nat Commun 16: 1276-1276

  • DOI: https://doi.org/10.1038/s41467-025-56612-4
  • Primary Citation of Related Structures:  
    8ZMH, 8ZMI, 8ZMJ, 8ZMK

  • PubMed 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 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.


  • Organizational Affiliation

    Department of Clinical Laboratory, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, The RNA Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tyrosine--tRNA ligase
A, B
379Phaseolus vulgarisMutation(s): 0 
Gene Names: PHAVU_002G027700g
EC: 6.1.1.1
UniProt
Find proteins for V7CJ18 (Phaseolus vulgaris)
Explore V7CJ18 
Go to UniProtKB:  V7CJ18
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV7CJ18
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release