1NHY | pdb_00001nhy

Crystal Structure of the GST-like Domain of Elongation Factor 1-gamma from Saccharomyces cerevisiae.

• PDB DOI: https://doi.org/10.2210/pdb1NHY/pdb

• Classification: TRANSLATION
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2002-12-20 Released: 2003-01-14 
• Deposition Author(s): Jeppesen, M.G., Ortiz, P., Kinzy, T.G., Andersen, G.R., Nyborg, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.235 (Depositor) 
• R-Value Work: 
  0.235 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Literature

The Crystal Structure of the Glutathione S-Transferase-like Domain of Elongation Factor 1B{gamma} from Saccharomyces cerevisiae.

Jeppesen, M.G., Ortiz, P., Shepard, W., Kinzy, T.G., Nyborg, J., Andersen, G.R.

(2003) J Biological Chem 278: 47190-47198

• PubMed: 12972429 
• DOI: https://doi.org/10.1074/jbc.M306630200
• Primary Citation Related Structures: 
  1NHY


• PubMed Abstract: 
  

  The crystal structure of the N-terminal 219 residues (domain 1) of the conserved eukaryotic translation elongation factor 1Bgamma (eEF1Bgamma), encoded by the TEF3 gene in Saccharomyces cerevisiae, has been determined at 3.0 A resolution by the single wavelength anomalous dispersion technique. The structure is overall very similar to the glutathione S-transferase proteins and contains a pocket with architecture highly homologous to what is observed in glutathione S-transferase enzymes. The TEF3-encoded form of eEF1Bgamma has no obvious catalytic residue. However, the second form of eEF1Bgamma encoded by the TEF4 gene contains serine 11, which may act catalytically. Based on the x-ray structure and gel filtration studies, we suggest that the yeast eEF1 complex is organized as an [eEF1A.eEF1Balpha.eEF1Bgamma]2 complex. A 23-residue sequence in the middle of eEF1Bgamma is essential for the stable dimerization of eEF1Bgamma and the quaternary structure of the eEF1 complex.

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Organizational Affiliation: 
• Department of Molecular Biology, University of Arhus, Gustav Wieds vej 10 C, 8000 Arhus C, Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 25.05 kDa 
• Atom Count: 1,753 
• Modeled Residue Count: 219 
• Deposited Residue Count: 219 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor 1-gamma 1	A	219	Saccharomyces cerevisiae	Mutation(s): 4  Gene Names: TEF3
UniProt
Find proteins for P29547 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P29547  Go to UniProtKB:  P29547

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.235 (Depositor) 
• R-Value Work:  0.235 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.52	α = 90
b = 164.52	β = 90
c = 164.52	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELXD	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-14 
Deposition Author(s): Jeppesen, M.G., Ortiz, P., Kinzy, T.G., Andersen, G.R., Nyborg, J.

Revision History  

• Version 1.0: 2003-01-14
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-13
  Changes: Data collection, Structure summary