5ME6 | pdb_00005me6

Crystal Structure of eiF4E from C. melo bound to a CAP analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.263 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

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Ligand Structure Quality Assessment 

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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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic transcription initiation factor 4E
A, B, C, D
186Cucumis meloMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.263 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.699α = 90
b = 108.868β = 90
c = 122.839γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted M7GClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MINECOSpainAGL2015-65838

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 2.0: 2024-05-08
    Changes: Data collection, Database references, Non-polymer description, Structure summary