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 
  • R-Value Observed: 0.239 

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:  
    5J5Y, 5J5O

  • 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 analogues containing dihalogenmethylenebisphosphonate moiety (i ...

    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: 

    Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4E A, B, C, D190Mus musculusMutation(s): 0 
Gene Names: Eif4e
Find proteins for P63073 (Mus musculus)
Explore P63073 
Go to UniProtKB:  P63073
NIH Common Fund Data Resources
IMPC:  MGI:95305
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6G6
Query on 6G6
Download Ideal Coordinates 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
GOL
Query on GOL
Download Ideal Coordinates CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6G6Ka:  82.80000305175781   M^-1  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.04α = 88.36
b = 38.06β = 95.63
c = 146.74γ = 103.54
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Higher EducationPolandDI2012 024842

Revision History  (Full details and data files)

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