4N3S

Crystal structure of eukaryotic translation initiation factor eIF5B (399-852) from Saccharomyces cerevisiae, apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.832 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

eIF5B employs a novel domain release mechanism to catalyze ribosomal subunit joining.

Kuhle, B.Ficner, R.

(2014) Embo J. 33: 1177-1191

  • DOI: 10.1002/embj.201387344
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • eIF5B is a eukaryal translational GTPase that catalyzes ribosomal subunit joining to form elongation-competent ribosomes. Despite its central role in protein synthesis, the mechanistic details that govern the function of eIF5B or its archaeal and bac ...

    eIF5B is a eukaryal translational GTPase that catalyzes ribosomal subunit joining to form elongation-competent ribosomes. Despite its central role in protein synthesis, the mechanistic details that govern the function of eIF5B or its archaeal and bacterial (IF2) orthologs remained unclear. Here, we present six high-resolution crystal structures of eIF5B in its apo, GDP- and GTP-bound form that, together with an analysis of the thermodynamics of nucleotide binding, provide a detailed picture of the entire nucleotide cycle performed by eIF5B. Our data show that GTP binding induces significant conformational changes in the two conserved switch regions of the G domain, resulting in the reorganization of the GTPase center. These rearrangements are accompanied by the rotation of domain II relative to the G domain and release of domain III from its stable contacts with switch 2, causing an increased intrinsic flexibility in the free GTP-bound eIF5B. Based on these data, we propose a novel domain release mechanism for eIF5B/IF2 activation that explains how eIF5B and IF2 fulfill their catalytic role during ribosomal subunit joining.


    Organizational Affiliation

    Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik Göttinger Zentrum für Molekulare Biowissenschaften Georg-August-Universität Göttingen, Göttingen, Germany bkuhle@gwdg.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 5B
A, B
457Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: FUN12
EC: 3.6.5.3
Find proteins for P39730 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39730
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.832 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.168 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 118.010α = 90.00
b = 118.010β = 90.00
c = 77.510γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-10-07 
  • Released Date: 2014-07-09 
  • Deposition Author(s): Kuhle, B., Ficner, R.

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-07-23
    Type: Other
  • Version 1.2: 2014-08-06
    Type: Structure summary
  • Version 1.3: 2018-03-07
    Type: Advisory, Data collection