6GKL

Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 2 (m7GppSpApG D2)

• PDB DOI: https://doi.org/10.2210/pdb6GKL/pdb

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


• Deposited: 2018-05-21 Released: 2019-06-19 
• Deposition Author(s): Warminski, M., Nowak, E., Kowalska, J., Jemielity, J., Nowotny, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.257 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Starting Model: experimental

Literature

Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 2 (m7GppSpApG D2)

Warminski, M., Nowak, E., Kubacka, D., Kowalska, J., Nowotny, M., Jemielity, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 93.31 kDa 
• Atom Count: 5,908 
• Modelled Residue Count: 727 
• Deposited Residue Count: 760 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 4E	A, B, C, D	190	Mus musculus	Mutation(s): 0  Gene Names: Eif4e
UniProt & NIH Common Fund Data Resources
Find proteins for P63073 (Mus musculus) Explore P63073  Go to UniProtKB:  P63073
IMPC:  MGI:95305

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G0Z	E [auth A], G [auth B], I [auth C], J [auth D]	[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-4,5-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate C31 H45 N15 O22 P4 S COVMLUYPZIGUSP-PEDZGMCBSA-N
GOL	F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.257 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.17	α = 88.8
b = 38.18	β = 84.67
c = 147.02	γ = 76.13

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-19 
Deposition Author(s): Warminski, M., Nowak, E., Kowalska, J., Jemielity, J., Nowotny, M.

---

Funding Organization	Location	Grant Number
	Poland	DI2012 024842
	Poland	ETIUDA 2017/24/T/NZ1/00345

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 2.0: 2019-10-23
  Changes: Data collection, Non-polymer description, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description