1EJ1

COCRYSTAL STRUCTURE OF THE MESSENGER RNA 5' CAP-BINDING PROTEIN (EIF4E) BOUND TO 7-METHYL-GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Cocrystal structure of the messenger RNA 5' cap-binding protein (eIF4E) bound to 7-methyl-GDP.

Marcotrigiano, J.Gingras, A.C.Sonenberg, N.Burley, S.K.

(1997) Cell 89: 951-961

  • DOI: 10.1016/s0092-8674(00)80280-9
  • Primary Citation of Related Structures:  
    1EJ1

  • PubMed Abstract: 
  • The X-ray structure of the eukaryotic translation initiation factor 4E (eIF4E), bound to 7-methyl-GDP, has been determined at 2.2 A resolution. eIF4E recognizes 5' 7-methyl-G(5')ppp(5')N mRNA caps during the rate-limiting initiation step of translation. The protein resembles a cupped hand and consists of a curved, 8-stranded antiparallel beta sheet, backed by three long alpha helices ...

    The X-ray structure of the eukaryotic translation initiation factor 4E (eIF4E), bound to 7-methyl-GDP, has been determined at 2.2 A resolution. eIF4E recognizes 5' 7-methyl-G(5')ppp(5')N mRNA caps during the rate-limiting initiation step of translation. The protein resembles a cupped hand and consists of a curved, 8-stranded antiparallel beta sheet, backed by three long alpha helices. 7-methyl-GDP binds in a narrow cap-binding slot on the molecule's concave surface, where 7-methyl-guanine recognition is mediated by base sandwiching between two conserved tryptophans, plus formation of three hydrogen bonds and a van der Waals contact between its N7-methyl group and a third conserved tryptophan. The convex dorsal surface of the molecule displays a phylogenetically conserved hydrophobic/acidic portion, which may interact with other translation initiation factors and regulatory proteins.


    Organizational Affiliation

    Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York 10021, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E AB190Mus musculusMutation(s): 0 
Gene Names: Eif4e
Find proteins for P63073 (Mus musculus)
Explore P63073 
Go to UniProtKB:  P63073
NIH Common Fund Data Resources
IMPC:  MGI:95305
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M7G
Query on M7G

Download Ideal Coordinates CCD File 
A, B
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
C11 H19 N5 O11 P2
QQODJOAVWUWVHJ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.6α = 90
b = 75.4β = 90
c = 76.6γ = 90
Software Package:
Software NamePurpose
SHELXSphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary