1L8B

Cocrystal Structure of the Messenger RNA 5' Cap-binding Protein (eIF4E) bound to 7-methylGpppG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Biophysical studies of eIF4E cap-binding protein: recognition of mRNA 5' cap structure and synthetic fragments of eIF4G and 4E-BP1 proteins.

Niedzwiecka, A.Marcotrigiano, J.Stepinski, J.Jankowska-Anyszka, M.Wyslouch-Cieszynska, A.Dadlez, M.Gingras, A.C.Mak, P.Darzynkiewicz, E.Sonenberg, N.Burley, S.K.Stolarski, R.

(2002) J.Mol.Biol. 319: 615-635

  • DOI: 10.1016/S0022-2836(02)00328-5

  • PubMed Abstract: 
  • mRNA 5'-cap recognition by the eukaryotic translation initiation factor eIF4E has been exhaustively characterized with the aid of a novel fluorometric, time-synchronized titration method, and X-ray crystallography. The association constant values of ...

    mRNA 5'-cap recognition by the eukaryotic translation initiation factor eIF4E has been exhaustively characterized with the aid of a novel fluorometric, time-synchronized titration method, and X-ray crystallography. The association constant values of recombinant eIF4E for 20 different cap analogues cover six orders of magnitude; with the highest affinity observed for m(7)GTP (approximately 1.1 x 10(8) M(-1)). The affinity of the cap analogues for eIF4E correlates with their ability to inhibit in vitro translation. The association constants yield contributions of non-covalent interactions involving single structural elements of the cap to the free energy of binding, giving a reliable starting point to rational drug design. The free energy of 7-methylguanine stacking and hydrogen bonding (-4.9 kcal/mol) is separate from the energies of phosphate chain interactions (-3.0, -1.9, -0.9 kcal/mol for alpha, beta, gamma phosphates, respectively), supporting two-step mechanism of the binding. The negatively charged phosphate groups of the cap act as a molecular anchor, enabling further formation of the intermolecular contacts within the cap-binding slot. Stabilization of the stacked Trp102/m(7)G/Trp56 configuration is a precondition to form three hydrogen bonds with Glu103 and Trp102. Electrostatically steered eIF4E-cap association is accompanied by additional hydration of the complex by approximately 65 water molecules, and by ionic equilibria shift. Temperature dependence reveals the enthalpy-driven and entropy-opposed character of the m(7)GTP-eIF4E binding, which results from dominant charge-related interactions (DeltaH degrees =-17.8 kcal/mol, DeltaS degrees= -23.6 cal/mol K). For recruitment of synthetic eIF4GI, eIF4GII, and 4E-BP1 peptides to eIF4E, all the association constants were approximately 10(7) M(-1), in decreasing order: eIF4GI>4E-BP1>eIF4GII approximately 4E-BP1(P-Ser65) approximately 4E-BP1(P-Ser65/Thr70). Phosphorylation of 4E-BP1 at Ser65 and Thr70 is insufficient to prevent binding to eIF4E. Enhancement of the eIF4E affinity for cap occurs after binding to eIF4G peptides.


    Organizational Affiliation

    Department of Biophysics, Institute of Experimental Physics, Warsaw University, 93 Zwirki & Wigury Street, 02-089 Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
A, B
190Mus musculusGene Names: Eif4e
Find proteins for P63073 (Mus musculus)
Go to UniProtKB:  P63073
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGP
Query on MGP

Download SDF File 
Download CCD File 
A, B
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE
C11 H19 N5 O14 P3
DKVRNHPCAOHRSI-KQYNXXCUSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MGPIC50: 2360 - 5720 nM (100) BINDINGDB
MGPKi: 28 nM (99) BINDINGDB
MGPKd: 10 nM (100) BINDINGDB
MGPKd: 140 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.120α = 90.00
b = 75.920β = 90.00
c = 77.840γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-12
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance