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 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 2.1 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: https://doi.org/10.1101/gad.269068.115
  • Primary Citation of Related Structures:  
    5ABU, 5ABV, 5ABX, 5ABY

  • 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. 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 Tübingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-3
A, C, E
190Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for O61955 (Caenorhabditis elegans)
Explore O61955 
Go to UniProtKB:  O61955
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO61955
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
4E-BINDING PROTEIN MEXTLI
B, D, F
41Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for Q9XW13 (Caenorhabditis elegans)
Explore Q9XW13 
Go to UniProtKB:  Q9XW13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XW13
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.24α = 90
b = 157.58β = 90
c = 55.18γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Database references
  • Version 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Other
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description