4NCL: Crystal structure of eukaryotic translation initiation factor eIF5B (517-970) from Chaetomium thermophilum in complex with GDP

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.
PDB ID: 4NCLDownload
MMDB ID: 121328
PDB Deposition Date: 2013/10/24
Updated in MMDB: 2014/08
Experimental Method:
x-ray diffraction
Resolution: 2.115  Å
Source Organism:
Similar Structures:
Biological Unit for 4NCL: monomeric; determined by author and by software (PISA)
Molecular Components in 4NCL
Label Count Molecule
Protein (1 molecule)
Eukaryotic Translation Initiation Factor 5b-like Protein(Gene symbol: CTHT_0029840)
Molecule annotation
Chemicals (2 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB