2ZU6

crystal structure of the eIF4A-PDCD4 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the eIF4A-PDCD4 complex

Chang, J.H.Cho, Y.H.Sohn, S.Y.Choi, J.M.Kim, A.Kim, Y.C.Jang, S.K.Cho, Y.

(2009) Proc.Natl.Acad.Sci.Usa 106: 3148-3153

  • DOI: 10.1073/pnas.0808275106

  • PubMed Abstract: 
  • Tumor suppressor programmed cell death protein 4 (PDCD4) inhibits the translation initiation factor eIF4A, an RNA helicase that catalyzes the unwinding of secondary structure at the 5'-untranslated region of mRNAs and controls the initiation of trans ...

    Tumor suppressor programmed cell death protein 4 (PDCD4) inhibits the translation initiation factor eIF4A, an RNA helicase that catalyzes the unwinding of secondary structure at the 5'-untranslated region of mRNAs and controls the initiation of translation. Here, we determined the crystal structure of the human eIF4A and PDCD4 complex. The structure reveals that one molecule of PDCD4 binds to the two eIF4A molecules through the two different binding modes. While the two MA3 domains of PDCD4 bind to one eIF4A molecule, the C-terminal MA3 domain alone of the same PDCD4 also interacts with another eIF4A molecule. The eIF4A-PDCD4 complex structure suggests that the MA3 domain(s) of PDCD4 binds perpendicular to the interface of the two domains of eIF4A, preventing the domain closure of eIF4A and blocking the binding of RNA to eIF4A, both of which are required events in the function of eIF4A helicase. The structure, together with biochemical analyses, reveals insights into the inhibition mechanism of eIF4A by PDCD4 and provides a framework for designing chemicals that target eIF4A.


    Organizational Affiliation

    National Creative Initiatives for Structural Biology and Department of Life Science, Pohang University of Science and Technology, Hyo-ja dong, San31, Pohang, KyungBook, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic initiation factor 4A-I
A, C, D, F
388Homo sapiensGene Names: EIF4A1 (DDX2A, EIF4A)
EC: 3.6.4.13
Find proteins for P60842 (Homo sapiens)
Go to Gene View: EIF4A1
Go to UniProtKB:  P60842
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Programmed cell death protein 4
B, E
307Homo sapiensGene Names: PDCD4 (H731)
Find proteins for Q53EL6 (Homo sapiens)
Go to Gene View: PDCD4
Go to UniProtKB:  Q53EL6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A, D
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
B, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.248 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 156.893α = 90.00
b = 165.384β = 90.00
c = 100.424γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXrefinement
HKL-3000data collection
HKL-3000data scaling
SHELXSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance