7WRU | pdb_00007wru

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

• PDB DOI: https://doi.org/10.2210/pdb7WRU/pdb

• Classification: TRANSLATION
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-01-27 Released: 2022-11-23 
• Deposition Author(s): Chung, S., Cho, Y.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.270 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

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

• PubMed: 36347866 
• DOI: https://doi.org/10.1038/s41467-022-34612-y
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.
Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea.
Postech Biotech Center, Pohang University of Science and Technology, Pohang, Republic of Korea.
Department of Oral Biochemistry, School of Dentistry, Pusan National University, Pusan, Republic of Korea.
Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, Republic of Korea.
Division of Biotechnology, Korea University, Seoul, Republic of Korea.
Institute of Life Science and Natural Resources, Korea University, Seoul, Republic of Korea.
Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea.
Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea.
Institute for Artificial Intelligence and Biomedical Research, College of Pharmacy, Gangnam Severance Hospital, Yonsei University, Incheon, 21983, Republic of Korea.
Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea. [e-mail].
Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea. [e-mail].
Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 61.56 kDa 
• Atom Count: 4,005 
• Modeled Residue Count: 493 
• Deposited Residue Count: 531 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamyl-tRNA synthetase	A	531	Gallus gallus	Mutation(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 A0A3Q2TSP8 (Gallus gallus) Explore A0A3Q2TSP8  Go to UniProtKB:  A0A3Q2TSP8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	B [auth A], C [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.270 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.044	α = 90
b = 41.762	β = 100.2
c = 92.186	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Chung, S., Cho, Y.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description