3RKQ

NKX2.5 Homeodomain dimer bound to ANF-242 DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 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

  • 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 comple ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Homeobox protein Nkx-2.5
A, B
58Homo sapiensMutation(s): 1 
Gene Names: NKX2-5 (CSX, NKX2.5, NKX2E)
Find proteins for P52952 (Homo sapiens)
Go to Gene View: NKX2-5
Go to UniProtKB:  P52952
Entity ID: 2
MoleculeChainsLengthOrganism
ANF-242 DNAC19N/A
Entity ID: 3
MoleculeChainsLengthOrganism
ANF-242 DNAD19N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.211 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 71.450α = 90.00
b = 71.450β = 90.00
c = 94.330γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
CNSrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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