3M94

Complex crystal structure of Ascaris suum eIF4E-3 with m2,2,7G cap


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1093/nar/gkr650
  • Primary Citation of Related Structures:  

  • 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-ca ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor 4E
A
189Ascaris suumMutation(s): 0 
Find proteins for Q6PKX2 (Ascaris suum)
Go to UniProtKB:  Q6PKX2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 4E-binding protein 1
C
17Homo sapiensMutation(s): 0 
Gene Names: EIF4EBP1
Find proteins for Q13541 (Homo sapiens)
Go to Gene View: EIF4EBP1
Go to UniProtKB:  Q13541
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M7M
Query on M7M

Download SDF File 
Download CCD File 
A
N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate)
C13 H23 N5 O11 P2
DHQQIEJARUGVNZ-WOUKDFQISA-N
 Ligand Interaction
ACE
Query on ACE

Download SDF File 
Download CCD File 
C
ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
M7MKd: 8400 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.204 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 104.977α = 90.00
b = 104.977β = 90.00
c = 46.906γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data collection
PHASESphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-20
    Type: Initial release
  • Version 1.1: 2011-10-12
    Type: Database references
  • Version 1.2: 2011-12-14
    Type: Database references