5X6G

Crystal Structure of SMAD5-MH1/palindromic SBE DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


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Literature

Structural basis for the Smad5 MH1 domain to recognize different DNA sequences.

Chai, N.Li, W.X.Wang, J.Wang, Z.X.Yang, S.M.Wu, J.W.

(2015) Nucleic Acids Res 43: 9051-9064

  • DOI: 10.1093/nar/gkv848
  • Primary Citation of Related Structures:  
    5X6M, 5X6H, 5X6G

  • PubMed Abstract: 
  • Smad proteins are important intracellular mediators of TGF-β signalling, which transmit signals directly from cell surface receptors to the nucleus. The MH1 domain of Smad plays a key role in DNA recognition. Two types of DNA sequence were identified as Smad binding motifs: the Smad binding element (SBE) and the GC-rich sequence ...

    Smad proteins are important intracellular mediators of TGF-β signalling, which transmit signals directly from cell surface receptors to the nucleus. The MH1 domain of Smad plays a key role in DNA recognition. Two types of DNA sequence were identified as Smad binding motifs: the Smad binding element (SBE) and the GC-rich sequence. Here we report the first crystal structure of the Smad5 MH1 domain in complex with the GC-rich sequence. Compared with the Smad5-MH1/SBE complex structure, the Smad5 MH1 domain contacts the GC-rich site with the same β-hairpin, but the detailed interaction modes are different. Conserved β-hairpin residues make base specific contacts with the minimal GC-rich site, 5'-GGC-3'. The assembly of Smad5-MH1 on the GC-rich DNA also results in distinct DNA conformational changes. Moreover, the crystal structure of Smad5-MH1 in complex with a composite DNA sequence demonstrates that the MH1 domain is targeted to each binding site (GC-rich or SBE) with modular binding modes, and the length of the DNA spacer affects the MH1 assembly. In conclusion, our work provides the structural basis for the recognition and binding specificity of the Smad MH1 domain with the DNA targets.


    Organizational Affiliation

    MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China jiaweiwu@mail.tsinghua.edu.cn.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mothers against decapentaplegic homolog 5A, B150Mus musculusMutation(s): 0 
Gene Names: Smad5Madh5Msmad5
UniProt
Find proteins for P97454 (Mus musculus)
Explore P97454 
Go to UniProtKB:  P97454
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*TP*CP*AP*GP*TP*CP*TP*AP*GP*AP*CP*AP*TP*A)-3')C16synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*GP*TP*AP*TP*GP*TP*CP*TP*AP*GP*AP*CP*TP*GP*A)-3')D16synthetic construct
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      E [auth A], F [auth B]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.05 Å
      • R-Value Free: 0.256 
      • R-Value Work: 0.223 
      • R-Value Observed: 0.224 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 71.535α = 90
      b = 74.502β = 90
      c = 83.74γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data collection
      HKL-2000data scaling
      PHASERphasing

      Structure Validation

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      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Natural Science Foundation of ChinaChina31130062
      China National Basic Research ProgramChina2013CB530600

      Revision History  (Full details and data files)

      • Version 1.0: 2017-03-15
        Type: Initial release