7WRU

Crystal structure of the apo chicken glutamyl-tRNA synthetase 1 (EARS1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Regulation of BRCA1 stability through the tandem UBX domains of isoleucyl-tRNA synthetase 1.

Chung, S.Kang, M.S.Alimbetov, D.S.Mun, G.I.Yunn, N.O.Kim, Y.Kim, B.G.Wie, M.Lee, E.A.Ra, J.S.Oh, J.M.Lee, D.Lee, K.Kim, J.Han, S.H.Kim, K.T.Chung, W.K.Nam, K.H.Park, J.Lee, B.Kim, S.Zhao, W.Ryu, S.H.Lee, Y.S.Myung, K.Cho, Y.

(2022) Nat Commun 13: 6732-6732

  • DOI: 10.1038/s41467-022-34612-y
  • Primary Citation of Related Structures:  
    7WRS, 7WRU

  • PubMed Abstract: 
  • Aminoacyl-tRNA synthetases (ARSs) have evolved to acquire various additional domains. These domains allow ARSs to communicate with other cellular proteins in order to promote non-translational functions. Vertebrate cytoplasmic isoleucyl-tRNA synthetases (IARS1s) have an uncharacterized unique domain, UNE-I ...

    Aminoacyl-tRNA synthetases (ARSs) have evolved to acquire various additional domains. These domains allow ARSs to communicate with other cellular proteins in order to promote non-translational functions. Vertebrate cytoplasmic isoleucyl-tRNA synthetases (IARS1s) have an uncharacterized unique domain, UNE-I. Here, we present the crystal structure of the chicken IARS1 UNE-I complexed with glutamyl-tRNA synthetase 1 (EARS1). UNE-I consists of tandem ubiquitin regulatory X (UBX) domains that interact with a distinct hairpin loop on EARS1 and protect its neighboring proteins in the multi-synthetase complex from degradation. Phosphomimetic mutation of the two serine residues in the hairpin loop releases IARS1 from the complex. IARS1 interacts with BRCA1 in the nucleus, regulates its stability by inhibiting ubiquitylation via the UBX domains, and controls DNA repair function.


    Organizational Affiliation

    Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea. yunje@postech.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamyl-tRNA synthetaseA531Gallus gallusMutation(s): 0 
Gene Names: RCJMB04_20b9
EC: 6.1.1.15 (PDB Primary Data), 6.1.1.17 (PDB Primary Data)
UniProt
Find proteins for Q5ZJ86 (Gallus gallus)
Explore Q5ZJ86 
Go to UniProtKB:  Q5ZJ86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZJ86
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.044α = 90
b = 41.762β = 100.2
c = 92.186γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release