5Y6L

A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and heterotetrameric glutathione transferase-homology domains in multi-tRNA synthetase complex

• PDB DOI: https://doi.org/10.2210/pdb5Y6L/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-08-12 Released: 2018-08-15 
• Deposition Author(s): Cho, H.Y., Lee, H.J., Kang, B.S.
• Funding Organization(s): National Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.252 
• R-Value Work: 0.176 
• R-Value Observed: 0.183 

Starting Models: experimental

Literature

A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and heterotetrameric glutathione transferase-homology domains in multi-tRNA synthetase complex

Cho, H.Y., Lee, H.J., Kang, B.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 152.86 kDa 
• Atom Count: 6,458 
• Modelled Residue Count: 825 
• Deposited Residue Count: 1,354 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine--tRNA ligase, cytoplasmic	A	232	Homo sapiens	Mutation(s): 1  Gene Names: MARS 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation elongation factor 1 epsilon-1	B	186	Homo sapiens	Mutation(s): 1  Gene Names: EEF1E1, AIMP3, P18
UniProt & NIH Common Fund Data Resources
Find proteins for O43324 (Homo sapiens) Explore O43324  Go to UniProtKB:  O43324
PHAROS:  O43324 GTEx:  ENSG00000124802

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional glutamate/proline--tRNA ligase	C	175	Homo sapiens	Mutation(s): 3  Gene Names: EPRS, GLNS, PARS, QARS, QPRS, PIG32 EC: 6.1.1.17 (PDB Primary Data), 6.1.1.15 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P07814 (Homo sapiens) Explore P07814  Go to UniProtKB:  P07814
PHAROS:  P07814 GTEx:  ENSG00000136628

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2	D	240	Homo sapiens	Mutation(s): 0  Gene Names: AIMP2, JTV1, PRO0992
UniProt & NIH Common Fund Data Resources
Find proteins for Q13155 (Homo sapiens) Explore Q13155  Go to UniProtKB:  Q13155
PHAROS:  Q13155 GTEx:  ENSG00000106305

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate--tRNA ligase, cytoplasmic	E	521	Homo sapiens	Mutation(s): 0  Gene Names: DARS, PIG40 EC: 6.1.1.12
UniProt & NIH Common Fund Data Resources
Find proteins for P14868 (Homo sapiens) Explore P14868  Go to UniProtKB:  P14868
PHAROS:  P14868 GTEx:  ENSG00000115866

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth A], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.252 
• R-Value Work: 0.176 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.535	α = 90
b = 98.413	β = 90
c = 125.919	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-15 
Deposition Author(s): Cho, H.Y., Lee, H.J., Kang, B.S.

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Funding Organization	Location	Grant Number
National Research Foundation	Korea, Republic Of	NRF-2014M3A6A4062857

Revision History  

• Version 1.0: 2018-08-15
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description