5Y6L | pdb_00005y6l

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.252 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history. 

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.

Macromolecule Content 

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

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Methionine--tRNA ligase, cytoplasmic232Homo sapiensMutation(s): 1 
Gene Names: MARS
EC: 6.1.1.10
UniProt & NIH Common Fund Data Resources
Find proteins for P56192 (Homo sapiens)
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Go to UniProtKB:  P56192
PHAROS:  P56192
GTEx:  ENSG00000166986 
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UniProt GroupP56192
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation elongation factor 1 epsilon-1186Homo sapiensMutation(s): 1 
Gene Names: EEF1E1, AIMP3, P18
UniProt & NIH Common Fund Data Resources
Find proteins for O43324 (Homo sapiens)
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Go to UniProtKB:  O43324
PHAROS:  O43324
GTEx:  ENSG00000124802 
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UniProt GroupO43324
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Bifunctional glutamate/proline--tRNA ligase175Homo sapiensMutation(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 
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UniProt GroupP07814
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2240Homo sapiensMutation(s): 0 
Gene Names: AIMP2, JTV1, PRO0992
UniProt & NIH Common Fund Data Resources
Find proteins for Q13155 (Homo sapiens)
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PHAROS:  Q13155
GTEx:  ENSG00000106305 
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UniProt GroupQ13155
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Aspartate--tRNA ligase, cytoplasmic521Homo sapiensMutation(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 
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UniProt GroupP14868
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.252 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.535α = 90
b = 98.413β = 90
c = 125.919γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research FoundationKorea, Republic OfNRF-2014M3A6A4062857

Revision History  (Full details and data files)

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