3EIJ

Crystal structure of Pdcd4

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural basis for translational inhibition by the tumour suppressor Pdcd4

Loh, P.G., Yang, H.-S., Walsh, M.A., Wang, Q., Wang, X., Cheng, Z., Liu, D., Song, H.

(2009) EMBO J 28: 274-285

  • DOI: 10.1038/emboj.2008.278
  • Primary Citation of Related Structures:  
    3EIQ, 3EIJ

  • PubMed Abstract: 

    • Pdcd4 is a tumour suppressor protein. It inhibits translation through interaction with translation initiator eIF4A, resulting in the suppression of neoplastic transformation and tumour invasion. Here, we present the crystal structures of an N-terminal-tr ...

    Pdcd4 is a tumour suppressor protein. It inhibits translation through interaction with translation initiator eIF4A, resulting in the suppression of neoplastic transformation and tumour invasion. Here, we present the crystal structures of an N-terminal-truncated Pdcd4 in free form and in complex with eIF4A. Upon binding to eIF4A, Pdcd4 undergoes a marked conformational change to form a heterotrimeric complex with eIF4A, with one Pdcd4 binding to two eIF4A molecules in two different modes. The binding of Pdcd4 to eIF4A is required to inhibit the enzymatic activity of eIF4A, translation initiation, and AP-1-dependent transcription. Both MA3 domains are required to efficiently compete with the C-terminal domain of eIF4G (eIF4Gc) for binding to eIF4A whereas a single MA3 is sufficient to inhibit translation. Our structural and mutational analyses reveal that Pdcd4 inhibits translation initiation by trapping eIF4A in an inactive conformation, and blocking its incorporation into the eIF4F complex.

    Organizational Affiliation: 

    Institute of Molecular and Cell Biology, Proteos, Singapore.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Programmed cell death protein 4 A, B321Homo sapiensMutation(s): 0 
Gene Names: PDCD4, H731
Find proteins for Q53EL6 (Homo sapiens)
Explore Q53EL6 
Go to UniProtKB:  Q53EL6
NIH Common Fund Data Resources
PHAROS:  Q53EL6
GTEx:  ENSG00000150593
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.325α = 90
b = 170.325β = 90
c = 66.919γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SHARPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2008-09-16 
  • Released Date: 2009-02-17 
    • Deposition Author(s): Loh, P.G.

Revision History 

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance