5ABY

Complex of C. elegans eIF4E-3 with the 4E-binding protein Mextli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mextli Proteins Use Both Canonical Bipartite and Novel Tripartite Binding Modes to Form Eif4E Complexes that Display Differential Sensitivity to 4E-BP Regulation

Peter, D.Weber, R.Koene, C.Chung, M.-Y.Ebertsch, L.Truffault, V.Weichenrieder, O.Igreja, C.Izaurralde, E.

(2015) Genes Dev. 29: 1835

  • DOI: 10.1101/gad.269068.115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The eIF4E-binding proteins (4E-BPs) are a diverse class of translation regulators that share a canonical eIF4E-binding motif (4E-BM) with eIF4G. Consequently, they compete with eIF4G for binding to eIF4E, thereby inhibiting translation initiation. Me ...

    The eIF4E-binding proteins (4E-BPs) are a diverse class of translation regulators that share a canonical eIF4E-binding motif (4E-BM) with eIF4G. Consequently, they compete with eIF4G for binding to eIF4E, thereby inhibiting translation initiation. Mextli (Mxt) is an unusual 4E-BP that promotes translation by also interacting with eIF3. Here we present the crystal structures of the eIF4E-binding regions of the Drosophila melanogaster (Dm) and Caenorhabditis elegans (Ce) Mxt proteins in complex with eIF4E in the cap-bound and cap-free states. The structures reveal unexpected evolutionary plasticity in the eIF4E-binding mode, with a classical bipartite interface for Ce Mxt and a novel tripartite interface for Dm Mxt. Both interfaces comprise a canonical helix and a noncanonical helix that engage the dorsal and lateral surfaces of eIF4E, respectively. Remarkably, Dm Mxt contains a C-terminal auxiliary helix that lies anti-parallel to the canonical helix on the eIF4E dorsal surface. In contrast to the eIF4G and Ce Mxt complexes, the Dm eIF4E-Mxt complexes are resistant to competition by bipartite 4E-BPs, suggesting that Dm Mxt can bind eIF4E when eIF4G binding is inhibited. Our results uncovered unexpected diversity in the binding modes of 4E-BPs, resulting in eIF4E complexes that display differential sensitivity to 4E-BP regulation.


    Organizational Affiliation

    Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 T├╝bingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-3
A, C, E
190Caenorhabditis elegansMutation(s): 0 
Gene Names: ife-3
Find proteins for O61955 (Caenorhabditis elegans)
Go to UniProtKB:  O61955
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
4E-BINDING PROTEIN MEXTLI
B, D, F
41Caenorhabditis elegansMutation(s): 0 
Gene Names: mxt-1 (mxt)
Find proteins for Q9XW13 (Caenorhabditis elegans)
Go to UniProtKB:  Q9XW13
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 91.240α = 90.00
b = 157.580β = 90.00
c = 55.180γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Database references