8J9S | pdb_00008j9s

leucine zipper complex of AIMP1 and AIMP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 
    0.273 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Assembly of the Human Multi-tRNA Synthetase Complex Through Leucine Zipper Motifs.

Kim, D.K.Lee, K.Kang, B.S.

(2024) J Mol Biology 436: 168865-168865

  • DOI: https://doi.org/10.1016/j.jmb.2024.168865
  • Primary Citation of Related Structures:  
    8J9S

  • PubMed Abstract: 

    Aminoacyl-tRNA synthetases (ARSs) are responsible for the ligation of amino acids to their cognate tRNAs. In human, nine ARSs form a multi-tRNA synthetase complex (MSC) with three ARS-interacting multifunctional proteins (AIMPs). Among the components of MSC, arginyl-tRNA synthetase 1 (RARS1) and two AIMPs (AIMP1 and AIMP2) have leucine zipper (LZ) motifs, which they utilize for their assembly in an MSC. RARS1 and AIMP1 have two LZ motifs (LZ1 and LZ2) in their N-terminus, respectively, while AIMP2 has one LZ motif between its lysyl-tRNA synthetase 1 (KARS1)-binding motif and glutathione transferase-homology domain, which links aspartyl-tRNA synthetase 1 (DARS1). Although the interaction mode between AIMP1 and RARS1, which also binds glutaminyl-tRNA synthetase 1 (QARS1), has been revealed, the mode in the presence of AIMP2 is still ambiguous since AIMP2 is known to not only bind to AIMP1 but also form a homodimer through its LZ. Here, we determined a crystal structure of the LZ complex of AIMP1 and AIMP2 and revealed the interaction mode of a heterotrimeric complex of RARS1, AIMP1, and AIMP2. The complex is established by a three-stranded coiled-coil structure with RARS1 LZ1, AIMP1 LZ1, and AIMP2 LZ and is completed with a two-stranded coiled-coil structure of RARS1 LZ2 and AIMP1 LZ2. In the human MSC, this heterotrimeric complex of RARS1, AIMP1, and AIMP2 allows for a subcomplex of fourteen protein molecules, in which two QARS1-RARS1-AIMP1-AIMP2-2 × KARS1 complexes are linked separately to a dimeric DARS1.


  • Organizational Affiliation
    • School of Life Science and Biotechnology, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoacyl tRNA synthase complex-interacting multifunctional protein 1
A, B
79Homo sapiensMutation(s): 0 
Gene Names: AIMP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q12904 (Homo sapiens)
Explore Q12904 
Go to UniProtKB:  Q12904
PHAROS:  Q12904
GTEx:  ENSG00000164022 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12904
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoacyl tRNA synthase complex-interacting multifunctional protein 249Homo sapiensMutation(s): 0 
Gene Names: AIMP2JTV1PRO0992
UniProt & NIH Common Fund Data Resources
Find proteins for Q13155 (Homo sapiens)
Explore Q13155 
Go to UniProtKB:  Q13155
PHAROS:  Q13155
GTEx:  ENSG00000106305 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13155
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.445α = 90
b = 95.445β = 90
c = 74.399γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2020R1A2C1003541

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-12-04
    Changes: Database references, Structure summary