5M7X | pdb_00005m7x

Translation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSepG mRNA 5' cap analog (beta-Se-ARCA D1)

• PDB DOI: https://doi.org/10.2210/pdb5M7X/pdb

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


• Deposited: 2016-10-28 Released: 2017-11-29 
• Deposition Author(s): Warminski, M., Nowak, E., Kowalska, J., Jemielity, J., Nowotny, M.
• Funding Organization(s): Ministry of Science and Higher Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Translation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSepG mRNA 5' cap analog (beta-Se-ARCA D1)

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 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: 91.23 kDa 
• Atom Count: 6,102 
• Modeled Residue Count: 695 
• 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
RSE	E [auth A], G [auth B], I [auth C], J [auth D]	[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl [phosphonooxy(selanyl)phosphoryl] hydrogen phosphate C12 H21 N5 O13 P3 Se FCPLZYTYUZTIIR-ZRDSBRMSSA-O
GOL	F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.11	α = 88.55
b = 38.16	β = 95.32
c = 147.07	γ = 103.33

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-29 
Deposition Author(s): Warminski, M., Nowak, E., Kowalska, J., Jemielity, J., Nowotny, M.

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Funding Organization	Location	Grant Number
Ministry of Science and Higher Education	Poland	DI2012 024842

Revision History  

• Version 1.0: 2017-11-29
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description