Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 25.18 kDa 
• Atom Count: 1891 
• Modelled Residue Count: 203 
• Deposited Residue Count: 212 
• Unique protein chains: 2

2JGB

Structure of human eIF4E homologous protein 4EHP with m7GTP

• DOI: 10.2210/pdb2JGB/pdb

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


• Deposited: 2007-02-12 Released: 2007-02-27 
• Deposition Author(s): Cameron, A.D., Rosettani, P., Knapp, S., Vismara, M.G., Rusconi, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.242 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Structures of the human eIF4E homologous protein, h4EHP, in its m7GTP-bound and unliganded forms.

Rosettani, P., Knapp, S., Vismara, M.G., Rusconi, L., Cameron, A.D.

(2007) J Mol Biol 368: 691-705

• PubMed: 17368478 
• DOI: 10.1016/j.jmb.2007.02.019
• Primary Citation of Related Structures:  
  2JGC, 2JGB


• PubMed Abstract: 
  

All eukaryotic cellular mRNAs contain a 5' m(7)GpppN cap. In addition to conferring stability to the mRNA, the cap is required for pre-mRNA splicing, nuclear export and translation by providing an anchor point for protein binding. In translation, the interaction between the cap and the eukaryotic initiation factor 4E (eIF4E) is important in the recruitment of the mRNAs to the ribosome. Human 4EHP (h4EHP) is a homologue of eIF4E. Like eIF4E it is able to bind the cap but it appears to play a different cellular role, possibly being involved in the fine-tuning of protein expression levels. Here we use X-ray crystallography and isothermal titration calorimetry (ITC) to investigate further the binding of cap analogues and peptides to h4EHP. m(7)GTP binds to 4EHP 200-fold more weakly than it does to eIF4E with the guanine base sandwiched by a tyrosine and a tryptophan instead of two tryptophan residues as seen in eIF4E. The tyrosine resides on a loop that is longer in h4EHP than in eIF4E. The consequent conformational difference between the proteins allows the tyrosine to mimic the six-membered ring of the tryptophan in eIF4E and adopt an orientation that is similar to that seen for equivalent residues in other non-homologous cap-binding proteins. In the absence of ligand the binding site is incompletely formed with one of the aromatic residues being disordered and the side-chain of the other adopting a novel conformation. A peptide derived from the eIF4E inhibitory protein, 4E-BP1 binds h4EHP 100-fold less strongly than eIF4E but in a similar manner. Overall the data, combined with sequence analyses of 4EHP from evolutionary diverse species, strongly support the hypothesis that 4EHP plays a physiological role utilizing both cap-binding and protein-binding functions but which is distinct from eIF4E.

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Organizational Affiliation: 

Department of Chemistry, Nerviano Medical Sciences S.r.l., viale Pasteur 10, 20014 Nerviano, Milan, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TYPE 2	A	195	Homo sapiens	Mutation(s): 0  Gene Names: EIF4E2, EIF4EL3
Find proteins for O60573 (Homo sapiens) Explore O60573  Go to UniProtKB:  O60573
NIH Common Fund Data Resources
PHAROS:  O60573 GTEx:  ENSG00000135930

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-BINDING PROTEIN 1	B	17	Homo sapiens	Mutation(s): 0  Gene Names: EIF4EBP1
Find proteins for Q13541 (Homo sapiens) Explore Q13541  Go to UniProtKB:  Q13541
NIH Common Fund Data Resources
PHAROS:  Q13541 GTEx:  ENSG00000187840

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGT	B	7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE C11 H20 N5 O14 P3 BUJQMJUTTBGELS-KQYNXXCUSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MGT	Ka:  410000   M^-1  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.242 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.499	α = 90
b = 49.299	β = 90
c = 103.767	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-02-12 
• Released Date: 2007-02-27 
Deposition Author(s): Cameron, A.D., Rosettani, P., Knapp, S., Vismara, M.G., Rusconi, L.

Revision History  

• Version 1.0: 2007-02-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-28
  Changes: Database references, Source and taxonomy