2HSN | pdb_00002hsn

Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.279 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes.

Simader, H.Hothorn, M.Kohler, C.Basquin, J.Simos, G.Suck, D.

(2006) Nucleic Acids Res 34: 3968-3979

  • DOI: https://doi.org/10.1093/nar/gkl560
  • Primary Citation Related Structures: 
    2HRK, 2HSM, 2HSN

  • PubMed Abstract: 

    The yeast aminoacyl-tRNA synthetase (aaRS) complex is formed by the methionyl- and glutamyl-tRNA synthetases (MetRS and GluRS, respectively) and the tRNA aminoacylation cofactor Arc1p. It is considered an evolutionary intermediate between prokaryotic aaRS and the multi- aaRS complex found in higher eukaryotes. While a wealth of structural information is available on the enzymatic domains of single aaRS, insight into complex formation between eukaryotic aaRS and associated protein cofactors is missing. Here we report crystal structures of the binary complexes between the interacting domains of Arc1p and MetRS as well as those of Arc1p and GluRS at resolutions of 2.2 and 2.05 A, respectively. The data provide a complete structural model for ternary complex formation between the interacting domains of MetRS, GluRS and Arc1p. The structures reveal that all three domains adopt a glutathione S-transferase (GST)-like fold and that simultaneous interaction of Arc1p with GluRS and MetRS is mediated by the use of a novel interface in addition to a classical GST dimerization interaction. The results demonstrate a novel role for this fold as a heteromerization domain specific to eukaryotic aaRS, associated proteins and protein translation elongation factors.


  • Organizational Affiliation
    • Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 32.21 kDa 
  • Atom Count: 2,355 
  • Modeled Residue Count: 280 
  • Deposited Residue Count: 282 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Methionyl-tRNA synthetase, cytoplasmic160Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MES1
EC: 6.1.1.10
UniProt
Find proteins for P00958 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00958 
Go to UniProtKB:  P00958
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00958
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GU4 nucleic-binding protein 1122Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ARC1
EC: 3.1.1
UniProt
Find proteins for P46672 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46672 
Go to UniProtKB:  P46672
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46672
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.279 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.48α = 90
b = 94.48β = 90
c = 88.47γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
SOLVEphasing
RESOLVEphasing
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description