1NK3

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    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

    Organizational Affiliation

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



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HOMEOBOX PROTEIN VNDC [auth P]77Drosophila melanogasterMutation(s): 0 
Gene Names: POTENTIALvndNK2CG6172
UniProt
Find proteins for P22808 (Drosophila melanogaster)
Explore P22808 
Go to UniProtKB:  P22808
Entity Groups  
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UniProt GroupP22808
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*GP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*CP*TP*GP*T)-3')A 16N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*CP*AP*GP*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*CP*A)-3')B 16N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 
  • OLDERADO: 1NK3 Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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