4S0H

TBX5 DB, NKX2.5 HD, ANF DNA Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Intermolecular Interactions of Cardiac Transcription Factors NKX2.5 and TBX5.

Pradhan, L.Gopal, S.Li, S.Ashur, S.Suryanarayanan, S.Kasahara, H.Nam, H.J.

(2016) Biochemistry 55: 1702-1710

  • DOI: 10.1021/acs.biochem.6b00171
  • Primary Citation of Related Structures:  
    4S0H, 5BQD

  • PubMed Abstract: 
  • Heart development in mammalian systems is controlled by combinatorial interactions of master cardiac transcription factors such as TBX5 and NKX2.5. They bind to promoters/enhancers of downstream targets as homo- or heteromultimeric complexes. They ph ...

    Heart development in mammalian systems is controlled by combinatorial interactions of master cardiac transcription factors such as TBX5 and NKX2.5. They bind to promoters/enhancers of downstream targets as homo- or heteromultimeric complexes. They physically interact and synergistically regulate their target genes. To elucidate the molecular basis of the intermolecular interactions, a heterodimer and a homodimer of NKX2.5 and TBX5 were studied using X-ray crystallography. Here we report a crystal structure of human NKX2.5 and TBX5 DNA binding domains in a complex with a 19 bp target DNA and a crystal structure of TBX5 homodimer. The ternary complex structure of NKX2.5 and TBX5 with the target DNA shows physical interactions between the two proteins through Lys158 (NKX2.5), Asp140 (TBX5), and Pro142 (TBX5), residues that are highly conserved in TBX and NKX families across species. Extensive homodimeric interactions were observed between the TBX5 proteins in both crystal structures. In particular, in the crystal structure of TBX5 protein that includes the N-terminal and DNA binding domains, intermolecular interactions were mediated by the N-terminal domain of the protein. The N-terminal domain of TBX5 was predicted to be "intrinsically unstructured", and in one of the two molecules in an asymmetric unit, the N-terminal domain assumes a β-strand conformation bridging two β-sheets from the two molecules. The structures reported here may represent general mechanisms for combinatorial interactions among transcription factors regulating developmental processes.


    Organizational Affiliation

    Department of Bioengineering, University of Texas at Dallas , Richardson, Texas 75080, United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein Nkx-2.5B, F53Homo sapiensMutation(s): 0 
Gene Names: NKX2-5CSXNKX2.5NKX2E
Find proteins for P52952 (Homo sapiens)
Explore P52952 
Go to UniProtKB:  P52952
NIH Common Fund Data Resources
PHAROS  P52952
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T-box transcription factor TBX5A, E186Homo sapiensMutation(s): 0 
Gene Names: TBX5
Find proteins for Q99593 (Homo sapiens)
Explore Q99593 
Go to UniProtKB:  Q99593
NIH Common Fund Data Resources
PHAROS  Q99593
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP*TP*GP*AP*AP*GP*TP*GP*G)-3'C, G19synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP*A)-3'D, H19synthetic construct
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.82 Å
      • R-Value Free: 0.247 
      • R-Value Work: 0.189 
      • R-Value Observed: 0.195 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 70.217α = 90
      b = 78.459β = 108.83
      c = 78.695γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data reduction

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      • Deposited Date: 2014-12-31 
      • Released Date: 2015-12-16 
      • Deposition Author(s): Pradhan, L.

      Revision History 

      • Version 1.0: 2015-12-16
        Type: Initial release
      • Version 1.1: 2016-03-16
        Changes: Database references
      • Version 1.2: 2016-04-13
        Changes: Database references