Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25934.38 
• Atom Count: 1772 
• Residue Count: 154 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

3RKQ

NKX2.5 Homeodomain dimer bound to ANF-242 DNA

• DOI: 10.2210/pdb3RKQ/pdb
• NDB: NA1097

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2011-04-18 Released: 2012-05-09 
• Deposition Author(s): Genis, C., Scone, P., Kasahara, H., Nam, H.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.257 
• R-Value Work: 0.211 

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

• PubMed: 22849347 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Homeobox protein Nkx-2.5	A, B	58	Homo sapiens	Mutation(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
Molecule	Chains	Length	Organism
ANF-242 DNA	C	19	N/A

Entity ID: 3
Molecule	Chains	Length	Organism
ANF-242 DNA	D	19	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 71.450	α = 90.00
b = 71.450	β = 90.00
c = 94.330	γ = 120.00

Software Package:

Software Name	Purpose
PHASER	phasing
HKL-2000	data reduction
HKL-2000	data scaling
CNS	refinement
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-18 
• Released Date: 2012-05-09 
• Deposition Author(s): Genis, C., Scone, P., Kasahara, H., Nam, H.-J.

Revision History 

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