5J5Y

Translation initiation factor 4E in complex with m2(7,2'O)GppCCl2ppG mRNA 5' cap analog

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history. 

Literature

mRNA cap analogues substituted in the tetraphosphate chain with CX2: identification of O-to-CCl2 as the first bridging modification that confers resistance to decapping without impairing translation.

Rydzik, A.M., Warminski, M., Sikorski, P.J., Baranowski, M.R., Walczak, S., Kowalska, J., Zuberek, J., Lukaszewicz, M., Nowak, E., W Claridge, T.D., Darzynkiewicz, E., Nowotny, M., Jemielity, J.

(2017) Nucleic Acids Res. 45: 8661-8675

  • DOI: 10.1093/nar/gkx569
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Analogues of the mRNA 5'-cap are useful tools for studying mRNA translation and degradation, with emerging potential applications in novel therapeutic interventions including gene therapy. We report the synthesis of novel mono- and dinucleotide cap a ...

    Analogues of the mRNA 5'-cap are useful tools for studying mRNA translation and degradation, with emerging potential applications in novel therapeutic interventions including gene therapy. We report the synthesis of novel mono- and dinucleotide cap analogues containing dihalogenmethylenebisphosphonate moiety (i.e. one of the bridging O atom substituted with CCl2 or CF2) and their properties in the context of cellular translational and decapping machineries, compared to phosphate-unmodified and previously reported CH2-substituted caps. The analogues were bound tightly to eukaryotic translation initiation factor 4E (eIF4E), with CCl2-substituted analogues having the highest affinity. When incorporated into mRNA, the CCl2-substituted dinucleotide most efficiently promoted cap-dependent translation. Moreover, the CCl2-analogues were potent inhibitors of translation in rabbit reticulocyte lysate. The crystal structure of eIF4E in complex with the CCl2-analogue revealed a significantly different ligand conformation compared to that of the unmodified cap analogue, which likely contributes to the improved binding. Both CCl2- and CF2- analogues showed lower susceptibility to hydrolysis by the decapping scavenger enzyme (DcpS) and, when incorporated into RNA, conferred stability against major cellular decapping enzyme (Dcp2) to transcripts. Furthermore, the use of difluoromethylene cap analogues was exemplified by the development of 19F NMR assays for DcpS activity and eIF4E binding.

    Organizational Affiliation: 

    Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 4E
A, B, C, D
190Mus musculusMutation(s): 0 
Gene Names: Eif4e
Find proteins for P63073 (Mus musculus)
Go to UniProtKB:  P63073
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
6G6
Query on 6G6
Download SDF File 
Download CCD File 
A, B
2-amino-9-{5-O-[(R)-{[(S)-{dichloro[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-O-methyl-beta-D-ribofuranosyl}-7-methyl-9H-purin-7-ium-6-olate
C13 H21 Cl2 N5 O16 P4
ULCNCADMRQHHSX-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 38.040α = 88.36
b = 38.060β = 95.63
c = 146.740γ = 103.54
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Higher EducationPolandDI2012 024842

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-07-12
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Advisory, Database references
  • Version 2.0: 2019-01-23
    Type: Advisory, Atomic model, Data collection