2HQT

Crystal structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA aminoacylation and nuclear export cofactor Arc1p reveal a novel function for an old fold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA-aminoacylation and nuclear-export cofactor Arc1p reveal a novel function for an old fold.

Simader, H.Hothorn, M.Suck, D.

(2006) ACTA CRYSTALLOGR.,SECT.D 62: 1510-1519

  • DOI: 10.1107/S0907444906039850
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Eukaryotic aminoacyl-tRNA synthetases (aaRS) frequently contain additional appended domains that are absent from their prokaryotic counterparts which mediate complex formation between eukaryotic aaRS and cofactors of aminoacylation and translation. H ...

    Eukaryotic aminoacyl-tRNA synthetases (aaRS) frequently contain additional appended domains that are absent from their prokaryotic counterparts which mediate complex formation between eukaryotic aaRS and cofactors of aminoacylation and translation. However, the structural basis of such interactions has remained elusive. The heteromerization domain of yeast glutamyl-tRNA synthetase (GluRS) has been cloned, expressed, purified and crystallized in space group C222(1), with unit-cell parameters a = 52, b = 107, c = 168 A. Phase information was obtained from multiple-wavelength anomalous dispersion with selenomethionine to 2.5 A resolution and the structure, comprising two monomers per asymmetric unit, was determined and refined to 1.9 A resolution. The structure of the interacting domain of its accessory protein Arc1p was determined and refined to 1.9 A resolution in a crystal form containing 20 monomers organized in five tetramers per asymmetric unit (space group C2, unit-cell parameters a = 222, b = 89, c = 127 A, beta = 99.4 degrees ). Both domains adopt a GST-like fold, demonstrating a novel role for this fold as a protein-protein interaction module.


    Related Citations: 
    • Expression, purification, crystallisation and preliminary phasing of the heteromerisation domain of the tRNA export and aminoacylation cofactor Arc1p from yeast
      Simader, H.,Suck, D.
      (2006) Acta Crystallogr.,Sect.F 62: 346
    • Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes
      Simader, H.,Hothorn, M.,Koehler, C.,Basquin, J.,Simos, G.,Suck, D.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GU4 nucleic-binding protein 1
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
124Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ARC1 (G4P1)
Find proteins for P46672 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P46672
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, E, I, J, M, N, Q, S
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 222.317α = 90.00
b = 89.463β = 99.39
c = 126.792γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SHELXCDphasing
SHELXDphasing
XSCALEdata scaling
XDSdata reduction
RESOLVEphasing
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description