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 

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:  

  • 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

    Center for the Science of Therapeutics, Broad Institute of MIT and Harvard , 415 Main St, Cambridge, MA, 02142, USA.,ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain. maria.macias@irbbarcelona.org.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.,EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain. maria.macias@irbbarcelona.org.,MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MH1 domain of human Smad4
A, B
135Homo sapiensMutation(s): 0 
Gene Names: SMAD4 (DPC4, MADH4)
Find proteins for Q13485 (Homo sapiens)
Go to Gene View: SMAD4
Go to UniProtKB:  Q13485
Entity ID: 2
MoleculeChainsLengthOrganism
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 SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
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 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 101.520α = 90.00
b = 101.520β = 90.00
c = 45.780γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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