3AM7

Crystal structure of the ternary complex of eIF4E-M7GTP-4EBP2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.230 

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Literature

Structural scaffold for eIF4E binding selectivity of 4E-BP isoforms: crystal structure of eIF4E binding region of 4E-BP2 and its comparison with that of 4E-BP1.

Fukuyo, A.In, Y.Ishida, T.Tomoo, K.

(2011) J Pept Sci 17: 650-657

  • DOI: https://doi.org/10.1002/psc.1384
  • Primary Citation of Related Structures:  
    3AM7

  • PubMed Abstract: 

    To clarify the higher eukaryotic initiation factor 4E (eIF4E) binding selectivity of 4E-binding protein 2 (4E-BP2) than of 4E-BP1, as determined by Trp fluorescence analysis, the crystal structure of the eIF4E binding region of 4E-BP2 in complex with m(7) GTP-bound human eIF4E has been determined by X-ray diffraction analysis and compared with that of 4E-BP1. The crystal structure revealed that the Pro47-Ser65 moiety of 4E-BP2 adopts a L-shaped conformation involving extended and α-helical structures and extends over the N-terminal loop and two different helix regions of eIF4E through hydrogen bonds, and electrostatic and hydrophobic interactions; these features were similarly observed for 4E-BP1. Although the pattern of the overall interaction of 4E-BP2 with eIF4E was similar to that of 4E-BP1, a notable difference was observed for the 60-63 sequence in relation to the conformation and binding selectivity of the 4E-BP isoform, i.e. Met-Glu-Cys-Arg for 4E-BP1 and Leu-Asp-Arg-Arg for 4E-BP2. In this paper, we report that the structural scaffold of the eIF4E binding preference for 4E-BP2 over 4E-BP1 is based on the stacking of the Arg63 planar side chain on the Trp73 indole ring of eIF4E and the construction of a compact hydrophobic space around the Trp73 indole ring by the Leu59-Leu60 sequence of 4E-BP2.


  • Organizational Affiliation

    Laboratory of Physical Chemistry, Osaka University of Pharmaceutical Sciences, Nasahara, Takatsuki, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4E191Homo sapiensMutation(s): 0 
Gene Names: EIF4EEIF4EL1EIF4F
UniProt & NIH Common Fund Data Resources
Find proteins for P06730 (Homo sapiens)
Explore P06730 
Go to UniProtKB:  P06730
PHAROS:  P06730
GTEx:  ENSG00000151247 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06730
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4E-binding protein 219Homo sapiensMutation(s): 0 
Gene Names: EIF4EBP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13542 (Homo sapiens)
Explore Q13542 
Go to UniProtKB:  Q13542
PHAROS:  Q13542
GTEx:  ENSG00000148730 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13542
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGP
Query on MGP

Download Ideal Coordinates CCD File 
C [auth A]7-METHYL-GUANOSINE-5'-TRIPHOSPHATE
C11 H19 N5 O14 P3
DKVRNHPCAOHRSI-KQYNXXCUSA-O
Binding Affinity Annotations 
IDSourceBinding Affinity
MGP BindingDB:  3AM7 Ki: 28 (nM) from 1 assay(s)
Kd: 10 (nM) from 1 assay(s)
IC50: min: 2360, max: 5720 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.230 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.84α = 90
b = 87.84β = 90
c = 37.75γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
CrystalCleardata reduction
SCALAdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-05-29
    Changes: Data collection