5XLN

Crystal structure of the TRS_UNE-T and 4EHP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/s41467-019-09086-0

  • 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 trans ...

    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

    Department of Biochemistry, Chungnam National University, Daejeon, 34134, Korea.,Department of Biochemistry, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.,Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea.,KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34141, Korea.,Personalized Genomic Medicine Research Center, KRIBB, Daejeon, 34141, Korea.,College of Pharmacy, Seoul National University, Seoul, 08826, Korea.,Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea. mhk8n@kribb.re.kr.,Dementia DTC R&D Convergence Program, Korea Institute of Science and Technology, Seoul, 02792, Korea.,Rosalind and Morris Goodman Cancer Research Centre, Montreal, Quebec, H3A 1A3, Canada.,Disease Target Structure Research Center, KRIBB, Daejeon, 34141, Korea.,College of Pharmacy, Seoul National University, Seoul, 08826, Korea. sungkim@snu.ac.kr.,Medicinal Bioconvergence Research Center, Seoul National University, Suwon, 16229, Korea. sungkim@snu.ac.kr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 4E type 2
A
190Homo sapiensMutation(s): 0 
Gene Names: EIF4E2 (EIF4EL3)
Find proteins for O60573 (Homo sapiens)
Go to Gene View: EIF4E2
Go to UniProtKB:  O60573
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Threonine--tRNA ligase, cytoplasmic
B
45Homo sapiensMutation(s): 0 
Gene Names: TARS
EC: 6.1.1.3
Find proteins for P26639 (Homo sapiens)
Go to Gene View: TARS
Go to UniProtKB:  P26639
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.369α = 90.00
b = 60.569β = 90.00
c = 85.237γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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