5M84 | pdb_00005m84

Translation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSpA mRNA 5' cap analog

• PDB DOI: https://doi.org/10.2210/pdb5M84/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-28 Released: 2017-12-20 
• 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: 1.85 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Translation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSpA mRNA 5' cap analog

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.

Macromolecule Content 

• Total Structure Weight: 46.11 kDa 
• Atom Count: 2,984 
• Modeled Residue Count: 357 
• 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  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
YDZ	C [auth A], F [auth B]	[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanyl-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate C22 H32 N10 O16 P3 S LVAVASOWNAXXPY-KVLYALRXSA-O
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.946	α = 90
b = 59.763	β = 95.84
c = 149.428	γ = 90

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: 2017-12-20 
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: 2017-12-20
  Type: Initial release
  
• Version 2.0: 2024-01-17
  Changes: Atomic model, Data collection, Database references, Refinement description