5NM9 image
Entry Detail
PDB ID:
5NM9
Keywords:
Title:
Crystal structure of the placozoa Trichoplax adhaerens Smad4-MH1 bound to the GGCGC site.
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2017-04-05
Release Date:
2017-11-15
Method Details:
Experimental Method:
Resolution:
2.43 Å
R-Value Free:
0.25
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Mothers against decapentaplegic homolog
Chain IDs:A, B
Chain Length:143
Number of Molecules:2
Biological Source:Trichoplax adhaerens
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3')
Chain IDs:C, D
Chain Length:18
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors.
Nat Commun 8 2070 2070 (2017)
PMID: 29234012 DOI: 10.1038/s41467-017-02054-6

Abstact

Smad transcription factors activated by TGF-β or by BMP receptors form trimeric complexes with Smad4 to target specific genes for cell fate regulation. The CAGAC motif has been considered as the main binding element for Smad2/3/4, whereas Smad1/5/8 have been thought to preferentially bind GC-rich elements. However, chromatin immunoprecipitation analysis in embryonic stem cells showed extensive binding of Smad2/3/4 to GC-rich cis-regulatory elements. Here, we present the structural basis for specific binding of Smad3 and Smad4 to GC-rich motifs in the goosecoid promoter, a nodal-regulated differentiation gene. The structures revealed a 5-bp consensus sequence GGC(GC)|(CG) as the binding site for both TGF-β and BMP-activated Smads and for Smad4. These 5GC motifs are highly represented as clusters in Smad-bound regions genome-wide. Our results provide a basis for understanding the functional adaptability of Smads in different cellular contexts, and their dependence on lineage-determining transcription factors to target specific genes in TGF-β and BMP pathways.

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