4BVX

Crystal structure of the AIMP3-MRS N-terminal domain complex with I3C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Assembly of Multi-tRNA Synthetase Complex Via Heterotetrameric Glutathione Transferase-Homology Domains.

Cho, H.Y.Maeng, S.J.Cho, H.J.Choi, Y.S.Chung, J.M.Lee, S.Kim, H.K.Kim, J.H.Eom, C.Kim, Y.Guo, M.Jung, H.S.Kang, B.S.Kim, S.

(2015) J Biol Chem 290: 29313

  • DOI: https://doi.org/10.1074/jbc.M115.690867
  • Primary Citation of Related Structures:  
    4BVX, 5A34, 5BMU

  • PubMed Abstract: 

    Many multicomponent protein complexes mediating diverse cellular processes are assembled through scaffolds with specialized protein interaction modules. The multi-tRNA synthetase complex (MSC), consisting of nine different aminoacyl-tRNA synthetases and three non-enzymatic factors (AIMP1-3), serves as a hub for many signaling pathways in addition to its role in protein synthesis. However, the assembly process and structural arrangement of the MSC components are not well understood. Here we show the heterotetrameric complex structure of the glutathione transferase (GST) domains shared among the four MSC components, methionyl-tRNA synthetase (MRS), glutaminyl-prolyl-tRNA synthetase (EPRS), AIMP2 and AIMP3. The MRS-AIMP3 and EPRS-AIMP2 using interface 1 are bridged via interface 2 of AIMP3 and EPRS to generate a unique linear complex of MRS-AIMP3:EPRS-AIMP2 at the molar ratio of (1:1):(1:1). Interestingly, the affinity at interface 2 of AIMP3:EPRS can be varied depending on the occupancy of interface 1, suggesting the dynamic nature of the linear GST tetramer. The four components are optimally arranged for maximal accommodation of additional domains and proteins. These characteristics suggest the GST tetramer as a unique and dynamic structural platform from which the MSC components are assembled. Considering prevalence of the GST-like domains, this tetramer can also provide a tool for the communication of the MSC with other GST-containing cellular factors.


  • Organizational Affiliation

    From the School of Life Science and Biotechnology, KNU Creative BioResearch Group, Kyungpook National University, Daegu 702-701, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
METHIONINE--TRNA LIGASE, CYTOPLASMIC215Homo sapiensMutation(s): 0 
EC: 6.1.1.10
UniProt & NIH Common Fund Data Resources
Find proteins for P56192 (Homo sapiens)
Explore P56192 
Go to UniProtKB:  P56192
PHAROS:  P56192
GTEx:  ENSG00000166986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56192
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1171Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for O43324 (Homo sapiens)
Explore O43324 
Go to UniProtKB:  O43324
PHAROS:  O43324
GTEx:  ENSG00000124802 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43324
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.284α = 90
b = 71.584β = 90
c = 116.381γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Data collection
  • Version 1.2: 2015-10-28
    Changes: Database references
  • Version 1.3: 2015-12-16
    Changes: Database references, Other, Structure summary
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other