5MEZ

Crystal structure of Smad4-MH1 bound to the GGCT site.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors.

Martin-Malpartida, P.Batet, M.Kaczmarska, Z.Freier, R.Gomes, T.Aragon, E.Zou, Y.Wang, Q.Xi, Q.Ruiz, L.Vea, A.Marquez, J.A.Massague, J.Macias, M.J.

(2017) Nat Commun 8: 2070-2070

  • DOI: https://doi.org/10.1038/s41467-017-02054-6
  • Primary Citation of Related Structures:  
    5MEY, 5MEZ, 5MF0, 5NM9, 5OD6, 5ODG

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Center for the Science of Therapeutics, Broad Institute of MIT and Harvard , 415 Main St, Cambridge, MA, 02142, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MH1 domain of human Smad4
A, B
135Homo sapiensMutation(s): 0 
Gene Names: SMAD4DPC4MADH4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13485 (Homo sapiens)
Explore Q13485 
Go to UniProtKB:  Q13485
GTEx:  ENSG00000141646 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13485
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3')C [auth D],
D [auth E]
16Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.79α = 90
b = 79.06β = 90
c = 114.16γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-12-27
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description