Trypanosoma cruzi EIF4E5 translation initiation factor in complex with m7GTP

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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Crystal structure of the Trypanosoma cruzi EIF4E5 translation factor homologue in complex with mRNA cap-4.

Reolon, L.W.Vichier-Guerre, S.de Matos, B.M.Dugue, L.Assuncao, T.R.D.S.Zanchin, N.I.T.Pochet, S.Guimaraes, B.G.

(2019) Nucleic Acids Res 47: 5973-5987

  • DOI: https://doi.org/10.1093/nar/gkz339
  • Primary Citation of Related Structures:  
    6O7Y, 6O7Z, 6O80

  • PubMed Abstract: 

    Association of the initiation factor eIF4E with the mRNA cap structure is a key step for translation. Trypanosomatids present six eIF4E homologues, showing a low conservation and also differing significantly from the IF4Es of multicellular eukaryotes. On the mRNA side, while in most eukaryotes the mRNA contains cap-0 (7-methyl-GTP), the trypanosomatid mRNA features a cap-4, which is formed by a cap-0, followed by the AACU sequence containing 2'-O-ribose methylations and base methylations on nucleotides 1 and 4. The studies on eIF4E-cap-4 interaction have been hindered by the difficulty to synthesize this rather elaborated cap-4 sequence. To overcome this problem, we applied a liquid-phase oligonucleotide synthesis strategy and describe for the first time the crystal structure of a trypanosomatid eIF4E (T. cruzi EIF4E5) in complex with cap-4. The TcEIF4E5-cap-4 structure allowed a detailed description of the binding mechanism, revealing the interaction mode for the AACU sequence, with the bases packed in a parallel stacking conformation and involved, together with the methyl groups, in hydrophobic contacts with the protein. This binding mechanism evidences a distinct cap interaction mode in comparison with previously described eIF4E structures and may account for the difference of TcEIF4E5-cap-4 dissociation constant in comparison with other eIF4E homologues.

  • Organizational Affiliation

    Biochemistry Postgraduate Program, Federal University of Parana, Curitiba, Paraná 81530-000, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative Eukaryotic translation initiation factor 4E type 5222Trypanosoma cruziMutation(s): 0 
Gene Names: C4B63_13g194
Find proteins for A0A2V2VRR6 (Trypanosoma cruzi)
Explore A0A2V2VRR6 
Go to UniProtKB:  A0A2V2VRR6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2V2VRR6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MGP

Download Ideal Coordinates CCD File 
C11 H19 N5 O14 P3
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
MGP Binding MOAD:  6O80 Kd: 2.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.59α = 90
b = 100.59β = 90
c = 40.61γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-03
    Changes: Data collection, Database references