5ME5 | pdb_00005me5

Crystal Structure of eiF4E from C. melo bound to a eIF4G peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.213 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

wwPDB Validation 3D Report Full Report

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Literature

Structure of eIF4E in Complex with an eIF4G Peptide Supports a Universal Bipartite Binding Mode for Protein Translation.

Miras, M.Truniger, V.Silva, C.Verdaguer, N.Aranda, M.A.Querol-Audi, J.

(2017) Plant Physiol 174: 1476-1491

  • DOI: https://doi.org/10.1104/pp.17.00193
  • Primary Citation Related Structures: 
    5ME5, 5ME6, 5ME7

  • PubMed Abstract: 

    The association-dissociation of the cap-binding protein eukaryotic translation initiation factor 4E (eIF4E) with eIF4G is a key control step in eukaryotic translation. The paradigm on the eIF4E-eIF4G interaction states that eIF4G binds to the dorsal surface of eIF4E through a single canonical alpha-helical motif, while metazoan eIF4E-binding proteins (m4E-BPs) advantageously compete against eIF4G via bimodal interactions involving this canonical motif and a second noncanonical motif of the eIF4E surface. Metazoan eIF4Gs share this extended binding interface with m4E-BPs, with significant implications on the understanding of translation regulation and the design of therapeutic molecules. Here we show the high-resolution structure of melon ( Cucumis melo ) eIF4E in complex with a melon eIF4G peptide and propose the first eIF4E-eIF4G structural model for plants. Our structural data together with functional analyses demonstrate that plant eIF4G binds to eIF4E through both the canonical and noncanonical motifs, similarly to metazoan eIF4E-eIF4G complexes. As in the case of metazoan eIF4E-eIF4G, this may have very important practical implications, as plant eIF4E-eIF4G is also involved in a significant number of plant diseases. In light of our results, a universal eukaryotic bipartite mode of binding to eIF4E is proposed.


  • Organizational Affiliation
    • Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), 30100 Espinardo, Murcia, Spain.

Macromolecule Content 

  • Total Structure Weight: 36.73 kDa 
  • Atom Count: 1,610 
  • Modeled Residue Count: 189 
  • Deposited Residue Count: 327 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic transcription initiation factor 4E237Cucumis meloMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
eIF4G90Cucumis meloMutation(s): 0 
UniProt
Find proteins for A0A1S3C4H6 (Cucumis melo)
Explore A0A1S3C4H6 
Go to UniProtKB:  A0A1S3C4H6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3C4H6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.213 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.094α = 90
b = 70.352β = 93.62
c = 42.798γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary