1.15 Angstrom Crystal Structure of the MA3 domain of Pdcd4

Experimental Data Snapshot

  • Resolution: 1.15 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 

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This is version 1.3 of the entry. See complete history


Structural basis for inhibition of translation by the tumor suppressor Pdcd4.

LaRonde-LeBlanc, N.Santhanam, A.N.Baker, A.R.Wlodawer, A.Colburn, N.H.

(2007) Mol Cell Biol 27: 147-156

  • DOI: https://doi.org/10.1128/MCB.00867-06
  • Primary Citation of Related Structures:  
    2IOL, 2ION, 2IOS, 2NSZ

  • PubMed Abstract: 

    The tumor suppressor function of Programmed Cell Death 4 (Pdcd4) is achieved through interactions between Pdcd4 and components of the translation initiation complex, namely, the RNA helicase eIF4A and the scaffolding protein eIF4G. These interactions are mediated through two MA3 domains on the Pdcd4 molecule and result in inhibition of protein synthesis. We have solved the high-resolution crystal structure of the C-terminal MA3 (cMA3) domain of Pdcd4 in several crystal forms and demonstrated its similarity to the MA3 domain of eIF4G. As predicted by the structure, the cMA3 domain competes with eIF4Gc for binding to eIF4A and surprisingly is sufficient to inhibit translation initiation. Mutations that abolish eIF4A binding negate both functions of the cMA3. Interestingly mutations in the Akt phosphorylation site influenced neither cMA3 binding to eIF4A nor its ability to inhibit translation initiation. Finally, our structural analysis reveals MA3 domains to be a novel subfamily of VHS domains.

  • Organizational Affiliation

    Macromolecular Crystallography Laboratory, CCR, National Cancer Institute, Frederick, MD 21702, USA. nlaronde@umd.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Programmed cell death protein 4129Mus musculusMutation(s): 0 
Gene Names: Pdcd4Ma3Tis
Find proteins for Q61823 (Mus musculus)
Explore Q61823 
Go to UniProtKB:  Q61823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ61823
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.15 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.52α = 90
b = 61.52β = 90
c = 77.751γ = 120
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description