3RKQ

NKX2.5 Homeodomain dimer bound to ANF-242 DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Crystal structure of the human NKX2.5 homeodomain in complex with DNA target.

Pradhan, L., Genis, C., Scone, P., Weinberg, E.O., Kasahara, H., Nam, H.J.

(2012) Biochemistry 51: 6312-6319

  • DOI: 10.1021/bi300849c
  • Primary Citation of Related Structures:  
    3RKQ

  • PubMed Abstract: 

    • NKX2.5 is a homeodomain containing transcription factor regulating cardiac formation and function, and its mutations are linked to congenital heart disease. Here we provide the first report of the crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene ...

    NKX2.5 is a homeodomain containing transcription factor regulating cardiac formation and function, and its mutations are linked to congenital heart disease. Here we provide the first report of the crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene. The crystal structure, determined at 1.8 Å resolution, demonstrates that NKX2.5 homeodomains occupy both DNA binding sites separated by five nucleotides without physical interaction between themselves. The two homeodomains show identical conformation despite the differences in the DNA sequences they bind, and no significant bending of the DNA was observed. Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif. This high resolution crystal structure of NKX2.5 protein provides a detailed picture of protein and DNA interactions, which allows us to predict DNA binding of mutants identified in human patients.

    Organizational Affiliation: 

    Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein Nkx-2.5A, B58Homo sapiensMutation(s): 1 
Gene Names: NKX2-5, CSX, NKX2.5, NKX2E
UniProt & NIH Common Fund Data Resources
Find proteins for P52952 (Homo sapiens)
Explore P52952 
Go to UniProtKB:  P52952
PHAROS:  P52952
GTEx:  ENSG00000183072
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    ANF-242 DNAC19N/A
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      ANF-242 DNAD19N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      MG
      Query on MG
      Download Ideal Coordinates CCD File 
      		 E [auth B]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.70 Å
      • R-Value Free: 0.257 
      • R-Value Work: 0.211 
      • Space Group: P 65
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 71.45α = 90
      b = 71.45β = 90
      c = 94.33γ = 120
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      PHASERphasing
      CNSrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2012-05-09
        Type: Initial release
      • Version 1.1: 2014-05-14
        Changes: Database references