5BMU

The crystal structure of the GST-like domains complex of AIMP3-EPRS mutant C92SC105SC123S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

wwPDB Validation   3D Report Full Report


This is version 1.3 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.Y.Kim, Y.G.Guo, M.Jung, H.S.Kang, B.S.Kim, S.

(2015) J Biol Chem 290: 29313-29328

  • 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
Eukaryotic translation elongation factor 1 epsilon-1
A, C, E, G
171Homo sapiensMutation(s): 0 
Gene Names: EEF1E1AIMP3P18
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate--tRNA ligase
B, D, F, H
175Homo sapiensMutation(s): 3 
Gene Names: EPRS
EC: 6.1.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P07814 (Homo sapiens)
Explore P07814 
Go to UniProtKB:  P07814
PHAROS:  P07814
GTEx:  ENSG00000136628 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07814
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.063α = 90
b = 92.063β = 90
c = 185.948γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-10-28
    Changes: Database references
  • Version 1.2: 2015-12-16
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description