1AHD

DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 16 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex.

Billeter, M.Qian, Y.Q.Otting, G.Muller, M.Gehring, W.Wuthrich, K.

(1993) J.Mol.Biol. 234: 1084-1097

  • DOI: 10.1006/jmbi.1993.1661

  • PubMed Abstract: 
  • The nuclear magnetic resonance (NMR) solution structure of a complex formed by the mutant Antennapedia homeodomain with Cys39 replaced by Ser, Antp(C39S), and a 14 base-pair DNA duplex containing the BS2 operator sequence was determined using uniform ...

    The nuclear magnetic resonance (NMR) solution structure of a complex formed by the mutant Antennapedia homeodomain with Cys39 replaced by Ser, Antp(C39S), and a 14 base-pair DNA duplex containing the BS2 operator sequence was determined using uniform 13C and 15N-labeling of the protein. Two-dimensional nuclear Overhauser enhancement spectroscopy ([1H,1H]NOESY) with 15N(omega 2)-half-filter and 13C(omega 1, omega 2)-double-half-filter, and three-dimensional heteronuclear-correlated [1H,1H]NOESY yielded a total of 855 intramolecular NOE upper distance constraints in the homeodomain, 151 upper distance constraints within the DNA duplex, and 39 intermolecular protein-DNA upper distance constraints. These data were used as the input for the structure calculation with simulated annealing followed by molecular dynamics in a water bath and energy refinement. A group of 16 conformers was thus generated which represent the solution structure of the Antp(C39S) homeodomain-DNA complex. The new structure determination confirms the salient features reported previously from a preliminary investigation of the same complex, in particular the location of the recognition helix in the major groove with the turn of the helix-turn-helix motif outside the contact area with the DNA, and the N-terminal arm of the homeodomain contacting the minor groove of the DNA. In addition, distinct amino acid side-chain-DNA contacts could be identified, and evidence was found that the invariant residue Asn51 (and possibly also Gln50) is in a slow dynamic equilibrium between two or several different DNA contact sites. The molecular dynamics calculations in a water bath yielded structures with hydration water molecules in the protein-DNA interface, which coincides with direct NMR observations of hydration waters. In the Appendix the experimental data obtained with the Antp(C39S) homeodomain-DNA complex and the techniques used for the structure calculation are evaluated using a simulated input data set derived from the X-ray crystal structure of a DNA complex with a homologous homeodomain. This study indicates that a nearly complete set of NOE upper distance constraints for the Antp(C39S) homeodomain and the protein-DNA interface was presently obtained. It further shows that the structure calculation used here yields a precise reproduction of the crystal structure from the simulated input data, and also results in hydration of the protein-DNA interface in the recalculated complex.


    Related Citations: 
    • The Structure of the Antennapedia Homeodomain Determined by NMR Spectroscopy in Solution: Comparison with Prokaryotic Repressors
      Qian, Y.-Q.,Billeter, M.,Otting, G.,Mueller, M.,Gehring, W.J.,Wuthrich, K.
      (1989) Cell 59: 573
    • Determination of the Three-Dimensional Structure of the Antennapedia Homeodomain from Drosophila in Solution by 1H Nuclear Magnetic Resonance Spectroscopy
      Billeter, M.,Qian, Y.-Q.,Otting, G.,Mueller, M.,Gehring, W.J.,Wuthrich, K.
      (1990) J.Mol.Biol. 214: 183
    • Protein-DNA Contacts in the Structure of a Homeodomain-DNA Complex Determined by Nuclear Magnetic Resonance Spectroscopy in Solution
      Otting, G.,Qian, Y.Q.,Billeter, M.,Mueller, M.,Affolter, M.,Gehring, W.J.,Wuthrich, K.
      (1990) Embo J. 9: 3085
    • Nuclear magnetic resonance spectroscopy of a DNA complex with the uniformly 13C-labeled Antennapedia homeodomain and structure determination of the DNA-bound homeodomain
      Qian, Y.Q.,Otting, G.,Billeter, M.,Mueller, M.,Gehring, W.J.,Wuthrich, K.
      (1993) J.Mol.Biol. 234: 1070


    Organizational Affiliation

    Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Homeotic protein antennapedia
P
68Drosophila subobscuraMutation(s): 1 
Gene Names: Antp
Find proteins for Q24645 (Drosophila subobscura)
Go to UniProtKB:  Q24645
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3')A14N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')B14N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 16 
  • Olderado: 1AHD Olderado
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2016-03-30
    Type: Structure summary