5X6H

Crystal Structure of SMAD5-MH1/GC-BRE DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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:  4ZKG, 4ZL2, 4ZL3, 5X6G, 5X6M

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mothers against decapentaplegic homolog 5
B
150Mus musculusGene Names: Smad5 (Madh5, Msmad5)
Find proteins for P97454 (Mus musculus)
Go to UniProtKB:  P97454
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*TP*AP*TP*GP*GP*CP*GP*CP*CP*AP*TP*AP*C)-3')E14synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.202 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.867α = 90.00
b = 92.867β = 90.00
c = 83.709γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

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