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 2.0 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: https://doi.org/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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
A, B
190Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P63073 (Mus musculus)
Explore P63073 
Go to UniProtKB:  P63073
IMPC:  MGI:95305
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63073
Sequence Annotations
Expand
  • 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],
D [auth B]
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
C11 H18 N5 O11 P2
SBASPRRECYVBRF-KQYNXXCUSA-O
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
  • Version 1.5: 2024-02-07
    Changes: Data collection, Database references
  • Version 2.0: 2024-03-06
    Changes: Data collection, Non-polymer description, Structure summary