PDBsum entry 2ful

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protein ligands Protein-protein interface(s) links
Translation PDB id
Protein chains
(+ 0 more) 161 a.a. *
SO4 ×20
Waters ×916
* Residue conservation analysis
PDB id:
Name: Translation
Title: Crystal structure of thE C-terminal domain of s. Cerevisiae
Structure: Eukaryotic translation initiation factor 5. Chain: a, b, c, d, e, f. Fragment: residues 236-412. Synonym: eif-5. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.50Å     R-factor:   0.177     R-free:   0.205
Authors: Z.Wei,Y.Xue,H.Xu,W.Gong
Key ref:
Z.Wei et al. (2006). Crystal structure of the C-terminal domain of S.cerevisiae eIF5. J Mol Biol, 359, 1-9. PubMed id: 16616930 DOI: 10.1016/j.jmb.2006.03.037
27-Jan-06     Release date:   23-May-06    
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Protein chains
Pfam   ArchSchema ?
P38431  (IF5_YEAST) -  Eukaryotic translation initiation factor 5
405 a.a.
161 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)


DOI no: 10.1016/j.jmb.2006.03.037 J Mol Biol 359:1-9 (2006)
PubMed id: 16616930  
Crystal structure of the C-terminal domain of S.cerevisiae eIF5.
Z.Wei, Y.Xue, H.Xu, W.Gong.
eIF5, a GTPase-activating protein (GAP) specific for eIF2, plays a critical role in pre-initiation complex assembly and correct AUG selection during eukaryotic translation initiation. eIF5 is involved in the formation of the multifactor complex (MFC), an important intermediate of the 43S pre-initiation complex. The C-terminal domain (CTD) of eIF5 functions as the structural core in the MFC assembly. Here we report the 1.5A crystal structure of eIF5-CTD, confirming that eIF5-CTD contains an atypical HEAT motif. In addition, analyzing the electrostatic potential and the distribution of conserved residues on the protein surface, we confirm and suggest some potential regions of interactions between eIF5-CTD and other eIFs. The structure of eIF5-CTD provides useful information in understanding the mechanism of the MFC assembly.
  Selected figure(s)  
Figure 1.
Figure 1. (a) Stereo view of the overall structure of the eIF5-CTD protomer. The four antiparallel helical repeats (R[I]-R[IV]) are colored in red, yellow, green, and blue, respectively. The 3[10]-helix y1 is colored in light green. The secondary structural elements are labeled in the left diagram. The disordered region is indicated by a broken line. No extra vector-encoded residues are included. See the text for details. (b) Diagrams of the eIF5-CTD trimer. The trimeric eIF5-CTD structure is constituted by protomers A, B, and C colored in yellow, purple, and salmon, respectively. The residues forming hydrogen bonds in the interfaces are presented in sticks and balls while the hydrogen bonds are shown as broken lines. The right diagram is a vertically inverted view of the left.
Figure 3.
Figure 3. (a) Electrostatic potential distribution on the surface of eIF5-CTD in different views. The surface is colored red for negative potential and blue for positive potential. Areas I, II and III are circled. (b) The CA model of eIF5-CTD with the same views of (a). The four repeats are colored as in Figure 1(a). The residues (marked in Figure 2(a) by triangles) on areas I, II and III are shown with their side-chains in top, middle and bottom diagrams, respectively.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 359, 1-9) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20485439 M.D.Jennings, and G.D.Pavitt (2010).
eIF5 has GDI activity necessary for translational control by eIF2 phosphorylation.
  Nature, 465, 378-381.  
17974565 M.Reibarkh, Y.Yamamoto, C.R.Singh, F.del Rio, A.Fahmy, B.Lee, R.E.Luna, M.Ii, G.Wagner, and K.Asano (2008).
Eukaryotic initiation factor (eIF) 1 carries two distinct eIF5-binding faces important for multifactor assembly and AUG selection.
  J Biol Chem, 283, 1094-1103.
PDB code: 2ogh
17512538 C.R.Singh, T.Udagawa, B.Lee, S.Wassink, H.He, Y.Yamamoto, J.T.Anderson, G.D.Pavitt, and K.Asano (2007).
Change in nutritional status modulates the abundance of critical pre-initiation intermediate complexes during translation initiation in vivo.
  J Mol Biol, 370, 315-330.  
17526738 S.S.Mohammad-Qureshi, R.Haddad, E.J.Hemingway, J.P.Richardson, and G.D.Pavitt (2007).
Critical contacts between the eukaryotic initiation factor 2B (eIF2B) catalytic domain and both eIF2beta and -2gamma mediate guanine nucleotide exchange.
  Mol Cell Biol, 27, 5225-5234.  
16990799 C.R.Singh, B.Lee, T.Udagawa, S.S.Mohammad-Qureshi, Y.Yamamoto, G.D.Pavitt, and K.Asano (2006).
An eIF5/eIF2 complex antagonizes guanine nucleotide exchange by eIF2B during translation initiation.
  EMBO J, 25, 4537-4546.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.