6GKJ

Translation initiation factor 4E in complex with trinucleotide mRNA 5' cap (m7GpppApG)

• PDB DOI: https://doi.org/10.2210/pdb6GKJ/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.249 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 

Literature

Translation initiation factor 4E in complex with trinucleotide mRNA 5' cap (m7GpppApG)

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 90.92 kDa 
• Atom Count: 6,047 
• Modelled Residue Count: 721 
• 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
MGP	E [auth A], G [auth B], I [auth C], J [auth D]	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE C11 H19 N5 O14 P3 DKVRNHPCAOHRSI-KQYNXXCUSA-O
GOL	F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MGP	BindingDB:  6GKJ	Ki: 28 (nM) from 1 assay(s)
		Kd: 10 (nM) from 1 assay(s)
		IC50: min: 2360, max: 5720 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.249 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.19	α = 84.18
b = 38.19	β = 88.55
c = 147.02	γ = 76.96

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.

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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 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description