2W97

Crystal Structure of eIF4E Bound to Glycerol and eIF4G1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystallization of eIF4E complexed with eIF4GI peptide and glycerol reveals distinct structural differences around the cap-binding site.

Brown, C.J.Verma, C.S.Walkinshaw, M.D.Lane, D.P.

(2009) Cell Cycle 8: 1905-1911

  • DOI: 10.4161/cc.8.12.8742
  • Primary Citation of Related Structures:  
    2W97

  • PubMed Abstract: 
  • An X-ray crystal structure of the eIF4E peptide complex is described in which two such complexes are located in the asymmetric unit. One of these complexes has m(7)GTP bound in a conformation which has been observed in several eIF4E crystal structures, whilst the other complex is free of m(7)GTP and contains a unique glycerol ...

    An X-ray crystal structure of the eIF4E peptide complex is described in which two such complexes are located in the asymmetric unit. One of these complexes has m(7)GTP bound in a conformation which has been observed in several eIF4E crystal structures, whilst the other complex is free of m(7)GTP and contains a unique glycerol. The two complexes show significant structural differences between each other in the cap-binding site. The glycerol bound structure shows a reorientation of the W102 side chain out of the cap-binding site, disordering of the W56 containing loop and rotation of the carboxyl side-chain of E103. This is accompanied by movement of the M101 side chain into a position where W56 in the m(7)GTP bound complex would otherwise occupy. Rotation of the W102 sidechain also displaces a structured water molecule to a new site. This novel conformation of eIF4E with glycerol bound is hypothesized to be an intermediate state between the apo and m(7)GTP bound forms of eIF4E. These insights should prove useful in the design of inhibitors of eIF4E for cancer therapy.


    Organizational Affiliation

    Institute of Molecular and Cell Biology (A-STAR), Proteos, Singapore.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 4EA217Homo sapiensMutation(s): 0 
Gene Names: EIF4EEIF4EL1EIF4F
Find proteins for P06730 (Homo sapiens)
Explore P06730 
Go to UniProtKB:  P06730
NIH Common Fund Data Resources
PHAROS:  P06730
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 4EB217Homo sapiensMutation(s): 0 
Gene Names: EIF4EEIF4EL1EIF4F
Find proteins for P06730 (Homo sapiens)
Explore P06730 
Go to UniProtKB:  P06730
NIH Common Fund Data Resources
PHAROS:  P06730
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA 1C [auth E], D [auth F]14Homo sapiensMutation(s): 0 
Gene Names: EIF4G1EIF4FEIF4GEIF4GI
Find proteins for Q04637 (Homo sapiens)
Explore Q04637 
Go to UniProtKB:  Q04637
NIH Common Fund Data Resources
PHAROS:  Q04637
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGO
Query on MGO

Download Ideal Coordinates CCD File 
E [auth A][[(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
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
F [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], J [auth B], K [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A], L [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GOLKd :  110000000   nM  PDBBind
MGOKd:  9   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.106α = 90
b = 38.201β = 101.51
c = 93.687γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-31
    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: 2019-10-09
    Changes: Data collection, Database references, Other