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 4R3Z | pdb_00004r3z

Crystal structure of human ArgRS-GlnRS-AIMP1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.03 Å
  • R-Value Free: 
    0.285 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4R3Z

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 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.

Macromolecule Content 

  • Total Structure Weight: 202.16 kDa 
  • Atom Count: 10,242 
  • Modeled Residue Count: 1,273 
  • Deposited Residue Count: 1,786 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aminoacyl tRNA synthase complex-interacting multifunctional protein 1312Homo sapiensMutation(s): 0 
Gene Names: AIMP1, EMAP2, SCYE1
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:|  3D Structure
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54136
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.03 Å
  • R-Value Free:  0.285 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
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

View Full Validation Report



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