1EJ1 | pdb_00001ej1

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

• PDB DOI: https://doi.org/10.2210/pdb1EJ1/pdb

• Classification: TRANSLATION
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-02-29 Released: 2000-03-15 
• Deposition Author(s): Marcotrigiano, J., Gingras, A.-C., Sonenberg, N., Burley, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.235 (Depositor), 0.362 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.344 (DCC) 

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

• PubMed: 9200613 
• DOI: https://doi.org/10.1016/s0092-8674(00)80280-9
• Primary Citation 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.

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Organizational Affiliation: 
• Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York 10021, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.21 kDa 
• Atom Count: 3,188 
• Modeled Residue Count: 368 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E	A, B	190	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P63073 (Mus musculus) Explore P63073  Go to UniProtKB:  P63073
IMPC:  MGI:95305

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M7G	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 (Depositor), 0.362 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.344 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.6	α = 90
b = 75.4	β = 90
c = 76.6	γ = 90

Software Package:

Software Name	Purpose
SHELXS	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-03-15 
Deposition Author(s): Marcotrigiano, J., Gingras, A.-C., Sonenberg, N., Burley, S.K.

Revision History  

• 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