6O7Y

Trypanosoma cruzi EIF4E5 translation initiation factor in complex with cap-4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.207 

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:  

  • 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 ...

    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.,Carlos Chagas Institute, Oswaldo Cruz Foundation, FIOCRUZ-PR, Curitiba, Paraná 81350-010, Brazil.,Unité de Chimie et Biocatalyse, Institut Pasteur, UMR3523 CNRS, Paris 75015, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative Eukaryotic translation initiation factor 4E type 5
A
222Trypanosoma cruziMutation(s): 0 
Find proteins for A0A2V2VRR6 (Trypanosoma cruzi)
Go to UniProtKB:  A0A2V2VRR6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LRM
Query on LRM

Download SDF File 
Download CCD File 
A
2-amino-9-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(S)-({(2R,3R,4R,5R)-3-{[(R)-{[(2R,3R,4R,5R)-3-{[(S)-{[(2R,3R,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-{[(S)-hydroxy{[(2R,3R,4R,5R)-3-hydroxy-4-methoxy-5-(3-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methoxy}phosphoryl]oxy}-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-(6-amino-9H-purin-9-yl)-4-methoxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-[6-(dimethylamino)-9H-purin-9-yl]-4-methoxytetrahydr
C56 H79 N20 O38 P6
LXUOPLSSKHEGET-DYPPLJCPSA-O
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.207 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.590α = 90.00
b = 102.590β = 90.00
c = 41.120γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
XDSdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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