The crystal structure of human cytoplasmic LRS

Experimental Data Snapshot

  • Resolution: 2.49 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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This is version 1.3 of the entry. See complete history


Molecular basis of the multifaceted functions of human leucyl-tRNA synthetase in protein synthesis and beyond.

Liu, R.J.Long, T.Li, H.Zhao, J.Li, J.Wang, M.Palencia, A.Lin, J.Cusack, S.Wang, E.D.

(2020) Nucleic Acids Res 48: 4946-4959

  • DOI: https://doi.org/10.1093/nar/gkaa189
  • Primary Citation of Related Structures:  
    6LPF, 6LR6

  • PubMed Abstract: 

    Human cytosolic leucyl-tRNA synthetase (hcLRS) is an essential and multifunctional enzyme. Its canonical function is to catalyze the covalent ligation of leucine to tRNALeu, and it may also hydrolyze mischarged tRNAs through an editing mechanism. Together with eight other aminoacyl-tRNA synthetases (AaRSs) and three auxiliary proteins, it forms a large multi-synthetase complex (MSC). Beyond its role in translation, hcLRS has an important moonlight function as a leucine sensor in the rapamycin complex 1 (mTORC1) pathway. Since this pathway is active in cancer development, hcLRS is a potential target for anti-tumor drug development. Moreover, LRS from pathogenic microbes are proven drug targets for developing antibiotics, which however should not inhibit hcLRS. Here we present the crystal structure of hcLRS at a 2.5 Å resolution, the first complete structure of a eukaryotic LRS, and analyze the binding of various compounds that target different sites of hcLRS. We also deduce the assembly mechanism of hcLRS into the MSC through reconstitution of the entire mega complex in vitro. Overall, our study provides the molecular basis for understanding both the multifaceted functions of hcLRS and for drug development targeting these functions.

  • Organizational Affiliation

    School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, P.R. China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine--tRNA ligase, cytoplasmic
A, B
1,092Homo sapiensMutation(s): 0 
Gene Names: LARSKIAA1352
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2J5 (Homo sapiens)
Explore Q9P2J5 
Go to UniProtKB:  Q9P2J5
GTEx:  ENSG00000133706 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P2J5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.49 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.217α = 90
b = 94.684β = 90
c = 680.055γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770842
National Natural Science Foundation of China (NSFC)China31971230

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-04-15
    Changes: Database references
  • Version 1.2: 2020-05-27
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Refinement description