1OZJ

Crystal structure of Smad3-MH1 bound to DNA at 2.4 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Features of a Smad3 MH1-DNA complex. Roles of water and zinc in DNA binding.

Chai, J., Wu, J.-W., Yan, N., Massague, J., Pavletich, N.P., Shi, Y.

(2003) J Biol Chem 278: 20327-20331

  • DOI: 10.1074/jbc.C300134200
  • Primary Citation of Related Structures:  
    1OZJ

  • PubMed Abstract: 

    • The Smad family of proteins mediates transforming growth factor-beta signaling from cell membrane to the nucleus. In the nucleus, Smads serve as transcription factors by directly binding to specific DNA sequences and regulating the expression of ligand-response genes ...

    The Smad family of proteins mediates transforming growth factor-beta signaling from cell membrane to the nucleus. In the nucleus, Smads serve as transcription factors by directly binding to specific DNA sequences and regulating the expression of ligand-response genes. A previous structural analysis, at 2.8-A resolution, revealed a novel DNA-binding mode for the Smad MH1 domain but did not allow accurate assignment of the fines features of protein-DNA interactions. The crystal structure of a Smad3 MH1 domain bound to a palindromic DNA sequence, determined at 2.4-A resolution, reveals a surprisingly important role for water molecules. The asymmetric placement of the DNA-binding motif (a conserved 11-residue beta-hairpin) in the major groove of DNA is buttressed by seven well ordered water molecules. These water molecules make specific hydrogen bonds to the DNA bases, the DNA phosphate backbones, and several critical Smad3 residues. In addition, the MH1 domain is found to contain a bound zinc atom using four invariant residues among Smad proteins, three cysteines and one histidine. Removal of the zinc atom results in compromised DNA binding activity. These results define the Smad MH1 domain as a zinc-coordinating module that exhibits unique DNA binding properties.

    Organizational Affiliation: 

    Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, New Jersey 08544, USA.



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SMAD 3C [auth A], D [auth B]144Homo sapiensMutation(s): 0 
Gene Names: MADH3 OR SMAD3 OR MAD3, SMAD3, MADH3
Find proteins for P84022 (Homo sapiens)
Explore P84022 
Go to UniProtKB:  P84022
NIH Common Fund Data Resources
PHAROS:  P84022
GTEx:  ENSG00000166949
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    Smad binding elementA [auth C]15N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      Smad binding elementB [auth D]15N/A
      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: 2.40 Å
      • R-Value Free: 0.270 
      • R-Value Work: 0.210 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 45.6α = 90
      b = 60.4β = 102
      c = 71.6γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      AMoREphasing
      CNSrefinement

      Structure Validation

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      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2004-03-23
        Type: Initial release
      • Version 1.1: 2008-04-29
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2018-04-04
        Changes: Data collection