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 1.3 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: https://doi.org/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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-box transcription factor TBX5A,
C [auth E]
186Homo sapiensMutation(s): 0 
Gene Names: TBX5
UniProt & NIH Common Fund Data Resources
Find proteins for Q99593 (Homo sapiens)
Explore Q99593 
Go to UniProtKB:  Q99593
PHAROS:  Q99593
GTEx:  ENSG00000089225 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99593
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Homeobox protein Nkx-2.5B,
D [auth F]
53Homo sapiensMutation(s): 0 
Gene Names: NKX2-5CSXNKX2.5NKX2E
UniProt & NIH Common Fund Data Resources
Find proteins for P52952 (Homo sapiens)
Explore P52952 
Go to UniProtKB:  P52952
PHAROS:  P52952
GTEx:  ENSG00000183072 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52952
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP*TP*GP*AP*AP*GP*TP*GP*G)-3'E [auth C],
G
19synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
5'-D(*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP*A)-3'F [auth D],
H
19synthetic construct
Sequence Annotations
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  • Reference Sequence
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

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references