5XLN

Crystal structure of the TRS_UNE-T and 4EHP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A threonyl-tRNA synthetase-mediated translation initiation machinery.

Jeong, S.J.Park, S.Nguyen, L.T.Hwang, J.Lee, E.Y.Giong, H.K.Lee, J.S.Yoon, I.Lee, J.H.Kim, J.H.Kim, H.K.Kim, D.Yang, W.S.Kim, S.Y.Lee, C.Y.Yu, K.Sonenberg, N.Kim, M.H.Kim, S.

(2019) Nat Commun 10: 1357-1357

  • DOI: https://doi.org/10.1038/s41467-019-09086-0
  • Primary Citation of Related Structures:  
    5XLN

  • PubMed Abstract: 

    A fundamental question in biology is how vertebrates evolved and differ from invertebrates, and little is known about differences in the regulation of translation in the two systems. Herein, we identify a threonyl-tRNA synthetase (TRS)-mediated translation initiation machinery that specifically interacts with eIF4E homologous protein, and forms machinery that is structurally analogous to the eIF4F-mediated translation initiation machinery via the recruitment of other translation initiation components. Biochemical and RNA immunoprecipitation analyses coupled to sequencing suggest that this machinery emerged as a gain-of-function event in the vertebrate lineage, and it positively regulates the translation of mRNAs required for vertebrate development. Collectively, our findings demonstrate that TRS evolved to regulate vertebrate translation initiation via its dual role as a scaffold for the assembly of initiation components and as a selector of target mRNAs. This work highlights the functional significance of aminoacyl-tRNA synthetases in the emergence and control of higher order organisms.


  • Organizational Affiliation

    Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4E type 2190Homo sapiensMutation(s): 0 
Gene Names: EIF4E2EIF4EL3
UniProt & NIH Common Fund Data Resources
Find proteins for O60573 (Homo sapiens)
Explore O60573 
Go to UniProtKB:  O60573
PHAROS:  O60573
GTEx:  ENSG00000135930 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60573
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Threonine--tRNA ligase, cytoplasmic45Homo sapiensMutation(s): 0 
Gene Names: TARS
EC: 6.1.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P26639 (Homo sapiens)
Explore P26639 
Go to UniProtKB:  P26639
PHAROS:  P26639
GTEx:  ENSG00000113407 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26639
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.369α = 90
b = 60.569β = 90
c = 85.237γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science, ICT & Future Planning of KoreaKorea, Republic OfNRF-2010-0029767
KRIBB Initiative ProgramKorea, Republic OfKGM4541622

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references