3M93

Complex crystal structure of Ascaris suum eIF4E-3 with m7G cap


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.245 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Literature

Structural basis for nematode eIF4E binding an m2,2,7G-Cap and its implications for translation initiation.

Liu, W.Jankowska-Anyszka, M.Piecyk, K.Dickson, L.Wallace, A.Niedzwiecka, A.Stepinski, J.Stolarski, R.Darzynkiewicz, E.Kieft, J.Zhao, R.Jones, D.N.Davis, R.E.

(2011) Nucleic Acids Res 39: 8820-8832

  • DOI: https://doi.org/10.1093/nar/gkr650
  • Primary Citation of Related Structures:  
    3M93, 3M94

  • PubMed Abstract: 

    Metazoan spliced leader (SL) trans-splicing generates mRNAs with an m(2,2,7)G-cap and a common downstream SL RNA sequence. The mechanism for eIF4E binding an m²²⁷G-cap is unknown. Here, we describe the first structure of an eIF4E with an m(2,2,7)G-cap and compare it to the cognate m⁷G-eIF4E complex. These structures and Nuclear Magnetic Resonance (NMR) data indicate that the nematode Ascaris suum eIF4E binds the two different caps in a similar manner except for the loss of a single hydrogen bond on binding the m(2,2,7)G-cap. Nematode and mammalian eIF4E both have a low affinity for m(2,2,7)G-cap compared with the m⁷G-cap. Nematode eIF4E binding to the m⁷G-cap, m(2,2,7)G-cap and the m(2,2,7)G-SL 22-nt RNA leads to distinct eIF4E conformational changes. Additional interactions occur between Ascaris eIF4E and the SL on binding the m(2,2,7)G-SL. We propose interactions between Ascaris eIF4E and the SL impact eIF4G and contribute to translation initiation, whereas these interactions do not occur when only the m(2,2,7)G-cap is present. These data have implications for the contribution of 5'-UTRs in mRNA translation and the function of different eIF4E isoforms.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor 4E189Ascaris suumMutation(s): 0 
Gene Names: Ascaris suum
UniProt
Find proteins for Q6PKX2 (Ascaris suum)
Explore Q6PKX2 
Go to UniProtKB:  Q6PKX2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PKX2
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4E-binding protein 1B [auth C]17Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13541 (Homo sapiens)
Explore Q13541 
Go to UniProtKB:  Q13541
PHAROS:  Q13541
GTEx:  ENSG00000187840 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13541
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M7G
Query on M7G

Download Ideal Coordinates CCD File 
C [auth A]7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
C11 H18 N5 O11 P2
SBASPRRECYVBRF-KQYNXXCUSA-O
Binding Affinity Annotations 
IDSourceBinding Affinity
M7G PDBBind:  3M93 Kd: 240 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.245 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.62α = 90
b = 104.62β = 90
c = 47.22γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PHASESphasing
REFMACrefinement
d*TREKdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-20
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Database references
  • Version 1.2: 2011-12-14
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2024-03-06
    Changes: Data collection, Non-polymer description, Structure summary