Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.17 kDa 
• Atom Count: 1,211 
• Modelled Residue Count: 95 
• Deposited Residue Count: 109 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 1NK3

VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, MINIMIZED AVERAGE STRUCTURE

• PDB DOI:  https://doi.org/10.2210/pdb1NK3/pdb
• NDB: 1NK3
• BMRB: 4141

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-05-06 Released: 1998-12-09 
• Deposition Author(s): Gruschus, J.M., Tsao, D.H.H., Wang, L.-H., Nirenberg, M., Ferretti, J.A.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 80 
• Conformers Submitted: 1 
• Selection Criteria: LEAST RESTRAINT VIOLATION 

Literature

Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity.

Gruschus, J.M., Tsao, D.H., Wang, L.H., Nirenberg, M., Ferretti, J.A.

(1997) Biochemistry 36: 5372-5380

• PubMed: 9154919 
• DOI: https://doi.org/10.1021/bi9620060
• Primary Citation of Related Structures:  
  1NK2, 1NK3


• PubMed Abstract: 
  

The interactions responsible for the nucleotide sequence-specific binding of the vnd/NK-2 homeodomain of Drosophila melanogaster to its consensus DNA binding site have been identified. A three-dimensional structure of the vnd/NK-2 homeodomain-DNA complex is presented, with emphasis on the structure of regions of observed protein-DNA contacts. This structure is based on protein-DNA distance restraints derived from NMR data, along with homology modeling, solvated molecular dynamics, and results from methylation and ethylation interference experiments. Helix III of the homeodomain binds in the major groove of the DNA and the N-terminal arm binds in the minor groove, in analogy with other homeodomain-DNA complexes whose structures have been reported. The vnd/NK-2 homeodomain recognizes the unusual DNA consensus sequence 5'-CAAGTG-3'. The roles in sequence specificity and strength of binding of individual amino acid residues that make contact with the DNA are described. We show, based primarily on the observed protein-DNA contacts, that the interaction of Y54 with the DNA is the major determinant of this uncommon nucleotide binding specificity in the vnd/NK-2 homeodomain-DNA complex.

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Related Citations: 

• Interactions of the Vnd/Nk-2 Homeodomain with DNA by Nuclear Magnetic Resonance Spectroscopy: Basis of Binding Specificity
  Gruschus, J.M., Tsao, D.H., Wang, L.H., Nirenberg, M., Ferretti, J.A.
  (1997) Biochemistry 36: 5372

• The Three-Dimensional Solution Structure of the Nk-2 Homeodomain from Drosophila
  Tsao, D.H., Gruschus, J.M., Wang, L.H., Nirenberg, M., Ferretti, J.A.
  (1995) J Mol Biol 251: 297

• Elongation of Helix III of the Nk-2 Homeodomain Upon Binding to DNA: A Secondary Structure Study by NMR
  Tsao, D.H., Gruschus, J.M., Wang, L.H., Nirenberg, M., Ferretti, J.A.
  (1994) Biochemistry 33: 15053

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Organizational Affiliation: 

Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-0380, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HOMEOBOX PROTEIN VND	C [auth P]	77	Drosophila melanogaster	Mutation(s): 0  Gene Names: POTENTIAL, vnd, NK2, CG6172
UniProt
Find proteins for P22808 (Drosophila melanogaster) Explore P22808  Go to UniProtKB:  P22808

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*CP*TP*GP*T)-3')	A	16	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*AP*GP*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*CP*A)-3')	B	16	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 80 
• Conformers Submitted: 1 
• Selection Criteria: LEAST RESTRAINT VIOLATION 

Structure Validation

Currently 1NK3 does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 1998-12-09 
Deposition Author(s): Gruschus, J.M., Tsao, D.H.H., Wang, L.-H., Nirenberg, M., Ferretti, J.A.

Revision History  

• Version 1.0: 1998-12-09
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Database references, Derived calculations, Other