6O7Z

Trypanosoma cruzi EIF4E5 translation initiation factor in complex with cap-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative Eukaryotic translation initiation factor 4E type 5A222Trypanosoma cruziMutation(s): 0 
Gene Names: C4B63_13g194
UniProt
Find proteins for A0A2V2VRR6 (Trypanosoma cruzi)
Explore A0A2V2VRR6 
Go to UniProtKB:  A0A2V2VRR6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LRP
Query on LRP

Download Ideal Coordinates CCD File 
B [auth A]2-amino-9-[(2R,3R,4S,5R)-5-({[(R)-{[(S)-{[(R)-({(2R,3R,4R,5R)-5-[6-(dimethylamino)-9H-purin-9-yl]-3-hydroxy-4-methoxytetrahydrofuran-2-yl}methoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]-7-methyl-6-oxo-6,9-dihydro-1H-purin-7-ium
C24 H36 N10 O17 P3
WWIREDRDOBXWDG-FRZFILDFSA-O
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.91α = 90
b = 102.91β = 90
c = 42.52γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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