4BVX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.217 

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.Kim, Y.Guo, M.Jung, H.S.Kang, B.S.Kim, S.

(2015) J.Biol.Chem. 290: 29313

  • DOI: 10.1074/jbc.M115.690867
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHIONINE--TRNA LIGASE, CYTOPLASMIC
A
215Homo sapiensMutation(s): 0 
Gene Names: MARS
EC: 6.1.1.10
Find proteins for P56192 (Homo sapiens)
Go to Gene View: MARS
Go to UniProtKB:  P56192
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1
B
171Homo sapiensMutation(s): 3 
Gene Names: EEF1E1 (AIMP3, P18)
Find proteins for O43324 (Homo sapiens)
Go to Gene View: EEF1E1
Go to UniProtKB:  O43324
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I3C
Query on I3C

Download SDF File 
Download CCD File 
A, B
5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid
5-Amino-2,4,6-triiodoisophthalic acid
C8 H4 I3 N O4
JEZJSNULLBSYHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.217 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.284α = 90.00
b = 71.584β = 90.00
c = 116.381γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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