Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 54.48 kDa 
• Atom Count: 3604 
• Modelled Residue Count: 402 
• Deposited Residue Count: 462 
• Unique protein chains: 2

4AZA

Improved eIF4E binding peptides by phage display guided design.

• PDB DOI: 10.2210/pdb4AZA/pdb

• Classification: TRANSLATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-25 Released: 2012-08-08 
• Deposition Author(s): Chew, W.Z., Quah, S.T., Verma, C.S., Liu, Y., Lane, D.P., Brown, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.279 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 

Literature

Improved Eif4E Binding Peptides by Phage Display Guided Design: Plasticity of Interacting Surfaces Yield Collective Effects.

Zhou, W., Quah, S.T., Verma, C.S., Liu, Y., Lane, D.P., Brown, C.J.

(2012) PLoS One 7: 47235

• PubMed: 23094039 
• DOI: 10.1371/journal.pone.0047235
• Primary Citation of Related Structures:  
  4AZA


• PubMed Abstract: 
  

Eukaryotic initiation factor (eIF)4E is over-expressed in many types of cancer such as breast, head and neck, and lung. A consequence of increased levels of eIF4E is the preferential translation of pro-tumorigenic proteins (e.g. c-Myc and vascular endothelial growth factor) and as a result is regarded as a potential therapeutic target. In this work a novel phage display peptide has been isolated against eIF4E. From the phage sequence two amino acids were delineated which improved binding when substituted into the eIF4G1 sequence. Neither of these substitutions were involved in direct interactions with eIF4E and acted either via optimization of the helical capping motif or restricting the conformational flexibility of the peptide. In contrast, substitutions of the remaining phage derived amino acids into the eIF4G1 sequence disrupted binding of the peptide to eIF4E. Interestingly when some of these disruptive substitutions were combined with key mutations from the phage peptide, they lead to improved affinities. Atomistic computer simulations revealed that the phage and the eIF4G1 derivative peptide sequences differ subtly in their interaction sites on eIF4E. This raises the issue, especially in the context of planar interaction sites such as those exhibited by eIF4E, that given the intricate plasticity of protein surfaces, the construction of structure-activity relationships should account for the possibility of significant movement in the spatial positioning of the peptide binding interface, including significant librational motions of the peptide.

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Organizational Affiliation: 

Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E	A, C	217	Homo sapiens	Mutation(s): 0  Gene Names: EIF4E, EIF4EL1, EIF4F
UniProt & NIH Common Fund Data Resources
Find proteins for P06730 (Homo sapiens) Explore P06730  Go to UniProtKB:  P06730
PHAROS:  P06730

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
EIF4G1_D5S PEPTIDE	B, D	14	Homo sapiens	Mutation(s): 0  Gene Names: EIF4G1, EIF4F, EIF4G, EIF4GI
UniProt & NIH Common Fund Data Resources
Find proteins for Q04637 (Homo sapiens) Explore Q04637  Go to UniProtKB:  Q04637
PHAROS:  Q04637

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGO	E [auth A], F [auth C]	[[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE C12 H20 N4 O14 P3 LPHBJZOLBGBNJF-XYHAGOFUSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.279 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.662	α = 90
b = 38.168	β = 90
c = 121.758	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM2	data reduction
PROTEUM2	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-25 
• Released Date: 2012-08-08 
Deposition Author(s): Chew, W.Z., Quah, S.T., Verma, C.S., Liu, Y., Lane, D.P., Brown, C.J.

Revision History  

• Version 1.0: 2012-08-08
  Type: Initial release
  
• Version 1.1: 2013-03-06
  Changes: Database references