4R3Z

Crystal structure of human ArgRS-GlnRS-AIMP1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.03 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the ArgRS-GlnRS-AIMP1 complex and its implications for mammalian translation

Fu, Y.Kim, Y.Jin, K.S.Kim, H.S.Kim, J.H.Wang, D.M.Park, M.Jo, C.H.Kwon, N.H.Kim, D.Kim, M.H.Jeon, Y.H.Hwang, K.Y.Kim, S.Cho, Y.

(2014) Proc Natl Acad Sci U S A 111: 15084-15089

  • DOI: https://doi.org/10.1073/pnas.1408836111
  • Primary Citation of Related Structures:  
    4R3Z

  • PubMed Abstract: 

    In higher eukaryotes, one of the two arginyl-tRNA synthetases (ArgRSs) has evolved to have an extended N-terminal domain that plays a crucial role in protein synthesis and cell growth and in integration into the multisynthetase complex (MSC). Here, we report a crystal structure of the MSC subcomplex comprising ArgRS, glutaminyl-tRNA synthetase (GlnRS), and the auxiliary factor aminoacyl tRNA synthetase complex-interacting multifunctional protein 1 (AIMP1)/p43. In this complex, the N-terminal domain of ArgRS forms a long coiled-coil structure with the N-terminal helix of AIMP1 and anchors the C-terminal core of GlnRS, thereby playing a central role in assembly of the three components. Mutation of AIMP1 destabilized the N-terminal helix of ArgRS and abrogated its catalytic activity. Mutation of the N-terminal helix of ArgRS liberated GlnRS, which is known to control cell death. This ternary complex was further anchored to AIMP2/p38 through interaction with AIMP1. These findings demonstrate the importance of interactions between the N-terminal domains of ArgRS and AIMP1 for the catalytic and noncatalytic activities of ArgRS and for the assembly of the higher-order MSC protein complex.


  • Organizational Affiliation

    Department of Life Science and.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoacyl tRNA synthase complex-interacting multifunctional protein 1312Homo sapiensMutation(s): 0 
Gene Names: AIMP1EMAP2SCYE1
UniProt & NIH Common Fund Data Resources
Find proteins for Q12904 (Homo sapiens)
Explore Q12904 
Go to UniProtKB:  Q12904
PHAROS:  Q12904
GTEx:  ENSG00000164022 
Entity Groups  
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UniProt GroupQ12904
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Arginine--tRNA ligase, cytoplasmic675Homo sapiensMutation(s): 0 
Gene Names: RARS
EC: 6.1.1.19
UniProt & NIH Common Fund Data Resources
Find proteins for P54136 (Homo sapiens)
Explore P54136 
Go to UniProtKB:  P54136
PHAROS:  P54136
GTEx:  ENSG00000113643 
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UniProt GroupP54136
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine--tRNA ligase799Homo sapiensMutation(s): 0 
Gene Names: QARS
EC: 6.1.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for P47897 (Homo sapiens)
Explore P47897 
Go to UniProtKB:  P47897
PHAROS:  P47897
GTEx:  ENSG00000172053 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47897
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.03 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.645α = 90
b = 313.253β = 90
c = 161.759γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Structure summary
  • Version 1.2: 2014-10-29
    Changes: Database references
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references