Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.57 kDa 
• Atom Count: 1431 
• Modelled Residue Count: 161 
• Deposited Residue Count: 189 
• Unique protein chains: 1

1PAQ

CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF EUKARYOTIC INITIATION FACTOR 2B EPSILON

• PDB DOI: 10.2210/pdb1PAQ/pdb

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


• Deposited: 2003-05-14 Released: 2004-02-10 
• Deposition Author(s): Boesen, T., Andersen, G.R., Pavitt, G.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.272 
• R-Value Work: 0.243 
• R-Value Observed: 0.244 

Literature

Structure of the catalytic fragment of translation initiation factor 2B and identification of a critically important catalytic residue.

Boesen, T., Mohammad, S.S., Pavitt, G.D., Andersen, G.R.

(2004) J Biol Chem 279: 10584-10592

• PubMed: 14681227 
• DOI: 10.1074/jbc.M311055200
• Primary Citation of Related Structures:  
  1PAQ


• PubMed Abstract: 
  

Eukaryotic initiation factor (eIF) 2B catalyzes the nucleotide activation of eIF2 to its active GTP-bound state. The exchange activity has been mapped to the C terminus of the eIF2Bepsilon subunit. We have determined the crystal structure of residues 544-704 from yeast eIF2Bepsilon at 2.3-A resolution, and this fragment is an all-helical protein built around the conserved aromatic acidic (AA) boxes also found in eIF4G and eIF5. The eight helices are organized in a manner similar to HEAT repeats. The molecule is highly asymmetric with respect to surface charge and conservation. One area in the N terminus is proposed to be directly involved in catalysis. In agreement with this hypothesis, mutation of glutamate 569 is shown to be lethal. An acidic belt and a second area in the C terminus containing residues from the AA boxes are important for binding to eIF2. Two mutations causing the fatal human genetic disease leukoencephalopathy with vanishing white matter are buried and appear to disrupt the structural integrity of the catalytic domain rather than interfering directly with catalysis or binding of eIF2.

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Organizational Affiliation: 

Department of Molecular Biology, Aarhus University, Denmark.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor eIF-2B epsilon subunit	A	189	Saccharomyces cerevisiae	Mutation(s): 5  Gene Names: GCD6 OR TIF225 OR YDR211W OR YD8142.12 OR YD8142B.03
UniProt
Find proteins for P32501 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32501  Go to UniProtKB:  P32501

Small Molecules

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: 2.30 Å
• R-Value Free: 0.272 
• R-Value Work: 0.243 
• R-Value Observed: 0.244 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.34	α = 90
b = 106.34	β = 90
c = 91.71	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-14 
• Released Date: 2004-02-10 
Deposition Author(s): Boesen, T., Andersen, G.R., Pavitt, G.D.

Revision History  

• Version 1.0: 2004-02-10
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance