2V8X

Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic and Mass Spectrometric Characterisation of Eif4E with N(7)-Alkylated CAP Derivatives.

Brown, C.J.Mcnae, I.Fischer, P.M.Walkinshaw, M.D.

(2007) J.Mol.Biol. 372: 7

  • DOI: 10.1016/j.jmb.2007.06.033
  • Primary Citation of Related Structures:  2V8W, 2V8Y

  • PubMed Abstract: 
  • Structural complexes of the eukaryotic translation initiation factor 4E (eIF4E) with a series of N(7)-alkylated guanosine derivative mRNA cap analogue structures have been characterised. Mass spectrometry was used to determine apparent gas-phase equi ...

    Structural complexes of the eukaryotic translation initiation factor 4E (eIF4E) with a series of N(7)-alkylated guanosine derivative mRNA cap analogue structures have been characterised. Mass spectrometry was used to determine apparent gas-phase equilibrium dissociation constants (K(d)) values of 0.15 microM, 13.6 microM, and 55.7 microM for eIF4E with 7-methyl-GTP (m(7)GTP), GTP, and GMP, respectively. For tight and specific binding to the eIF4E mononucleotide binding site, there seems to be a clear requirement for guanosine derivatives to possess both the delocalised positive charge of the N(7)-methylated guanine system and at least one phosphate group. We show that the N(7)-benzylated monophosphates 7-benzyl-GMP (Bn(7)GMP) and 7-(p-fluorobenzyl)-GMP (FBn(7)GMP) bind eIF4E substantially more tightly than non-N(7)-alkylated guanosine derivatives (K(d) values of 7.0 microM and 2.0 microM, respectively). The eIF4E complex crystal structures with Bn(7)GMP and FBn(7)GMP show that additional favourable contacts of the benzyl groups with eIF4E contribute binding energy that compensates for loss of the beta and gamma-phosphates. The N(7)-benzyl groups pack into a hydrophobic pocket behind the two tryptophan side-chains that are involved in the cation-pi stacking interaction between the cap and the eIF4E mononucleotide binding site. This pocket is formed by an induced fit in which one of the tryptophan residues involved in cap binding flips through 180 degrees relative to structures with N(7)-methylated cap derivatives. This and other observations made here will be useful in the design of new families of eIF4E inhibitors, which may have potential therapeutic applications in cancer.


    Organizational Affiliation

    Structural Biochemistry, The University of Edinburgh, Michael Swann Building, King's Buildings, Edinburgh, EH9 3JR, Scotland, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
A, E
217Homo sapiensGene Names: EIF4E (EIF4EL1, EIF4F)
Find proteins for P06730 (Homo sapiens)
Go to Gene View: EIF4E
Go to UniProtKB:  P06730
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-BINDING PROTEIN 1
B, F
14Homo sapiensGene Names: EIF4EBP1
Find proteins for Q13541 (Homo sapiens)
Go to Gene View: EIF4EBP1
Go to UniProtKB:  Q13541
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGQ
Query on MGQ

Download SDF File 
Download CCD File 
A, E
7-BENZYL GUANINE MONOPHOSPHATE
C17 H21 N5 O8 P
WMKJRKYLDWLLPS-XNIJJKJLSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MGQIC50: 15500 - 26800 nM (100) BINDINGDB
MGQKd: 790 - 1320 nM (98) BINDINGDB
MGQKd: 6950 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.256α = 90.00
b = 100.213β = 90.00
c = 135.209γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance