5MF0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/s41467-017-02054-6
  • Primary Citation of Related Structures:  
    5MEZ, 5MEY, 5MF0, 5NM9, 5ODG, 5OD6

  • 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 h ...

    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

    ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain. maria.macias@irbbarcelona.org.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MH1 domain of human Smad4AB135Homo sapiensMutation(s): 0 
Gene Names: SMAD4DPC4MADH4
Find proteins for Q13485 (Homo sapiens)
Explore Q13485 
Go to UniProtKB:  Q13485
NIH Common Fund Data Resources
PHAROS  Q13485
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*GP*CP*CP*CP*GP*T)-3')E, F16Homo sapiens
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download CCD File 
    A, B
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    CL
    Query on CL

    Download CCD File 
    A, B
    CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.03 Å
    • R-Value Free: 0.270 
    • R-Value Work: 0.231 
    • R-Value Observed: 0.232 
    • Space Group: P 43
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 101.52α = 90
    b = 101.52β = 90
    c = 45.78γ = 90
    Software Package:
    Software NamePurpose
    BUSTERrefinement
    XDSdata reduction
    XSCALEdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2017-11-15
      Type: Initial release
    • Version 1.1: 2017-12-27
      Changes: Database references