Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 119.51 kDa 
• Atom Count: 7392 
• Modelled Residue Count: 861 
• Deposited Residue Count: 1042 
• Unique protein chains: 1

4J15

Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex

• PDB DOI: 10.2210/pdb4J15/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-01 Released: 2013-05-15 
• Deposition Author(s): Kim, K.R., Park, S.H., Kim, H.S., Kim, B.-G., Kim, D.G., Rhee, K.H., Park, M.S., Kim, H.-J., Kim, S., Han, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.228 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex

Kim, K.R., Park, S.H., Kim, H.S., Rhee, K.H., Kim, B.-G., Kim, D.G., Park, M.S., Kim, H.-J., Kim, S., Han, B.W.

(2013) Proteins 81: 1840-1846

• PubMed: 23609930 
• DOI: 10.1002/prot.24306
• Primary Citation of Related Structures:  
  4J15


• PubMed Abstract: 
  

Human cytosolic aspartyl-tRNA synthetase (DRS) catalyzes the attachment of the amino acid aspartic acid to its cognate tRNA and it is a component of the multi-tRNA synthetase complex (MSC) which has been known to be involved in unexpected signaling pathways. Here, we report the crystal structure of DRS at a resolution of 2.25 Å. DRS is a homodimer with a dimer interface of 3750.5 Å(2) which comprises 16.6% of the monomeric surface area. Our structure reveals the C-terminal end of the N-helix which is considered as a unique addition in DRS, and its conformation further supports the switching model of the N-helix for the transfer of tRNA(Asp) to elongation factor 1α. From our analyses of the crystal structure and post-translational modification of DRS, we suggest that the phosphorylation of Ser146 provokes the separation of DRS from the MSC and provides the binding site for an interaction partner with unforeseen functions.

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Organizational Affiliation: 

Research Institute of Pharmaceutical Sciences, Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, 151-742, Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate--tRNA ligase, cytoplasmic	A, B	521	Homo sapiens	Mutation(s): 0  Gene Names: DARS, DARS1, 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.228 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.885	α = 90
b = 141.921	β = 102.19
c = 68.495	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-01 
• Released Date: 2013-05-15 
Deposition Author(s): Kim, K.R., Park, S.H., Kim, H.S., Kim, B.-G., Kim, D.G., Rhee, K.H., Park, M.S., Kim, H.-J., Kim, S., Han, B.W.

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2013-10-16
  Changes: Database references