2V8Y

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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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, 2V8X, 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 equilibrium dissociation constants (K(d)) values of 0 ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E A, E217Homo sapiensMutation(s): 0 
Gene Names: EIF4E, EIF4EL1, EIF4F
Find proteins for P06730 (Homo sapiens)
Explore P06730 
Go to UniProtKB:  P06730
NIH Common Fund Data Resources
PHAROS:  P06730
GTEx:  ENSG00000151247
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-BINDING PROTEIN 1 B, F14Homo sapiensMutation(s): 0 
Gene Names: EIF4EBP1
Find proteins for Q13541 (Homo sapiens)
Explore Q13541 
Go to UniProtKB:  Q13541
NIH Common Fund Data Resources
PHAROS:  Q13541
GTEx:  ENSG00000187840
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGV
Query on MGV
Download Ideal Coordinates CCD File 
A, E
P-FLUORO-7-BENZYL GUANINE MONOPHOSPHATE
C17 H20 F N5 O8 P
VLABRVWLURSKLS-XNIJJKJLSA-O		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MGVKd:  7510   nM  BindingDB
MGVKd:  8220   nM  BindingDB
MGVKd:  1960   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.438α = 90
b = 100.731β = 90
c = 135.334γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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