1ahd: Difference between revisions

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[[Image:1ahd.gif|left|200px]]


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==DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX==
The line below this paragraph, containing "STRUCTURE_1ahd", creates the "Structure Box" on the page.
<StructureSection load='1ahd' size='340' side='right'caption='[[1ahd]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1ahd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_subobscura Drosophila subobscura]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AHD FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ahd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ahd OCA], [https://pdbe.org/1ahd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ahd RCSB], [https://www.ebi.ac.uk/pdbsum/1ahd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ahd ProSAT]</span></td></tr>
{{STRUCTURE_1ahd|  PDB=1ahd  |  SCENE= }}
</table>
 
== Function ==
'''DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX'''
[https://www.uniprot.org/uniprot/ANTP_DROSU ANTP_DROSU] Sequence-specific transcription factor which is part of a developmental regulatory system that regulates segmental identity in the mesothorax. Provides cells with specific positional identities on the anterior-posterior axis (By similarity).[UniProtKB:P02833]
 
== Evolutionary Conservation ==
 
[[Image:Consurf_key_small.gif|200px|right]]
==Overview==
Check<jmol>
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.
  <jmolCheckbox>
 
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ah/1ahd_consurf.spt"</scriptWhenChecked>
==About this Structure==
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
1AHD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AHD OCA].  
    <text>to colour the structure by Evolutionary Conservation</text>
 
  </jmolCheckbox>
==Reference==
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ahd ConSurf].
Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex., Billeter M, Qian YQ, Otting G, Muller M, Gehring W, Wuthrich K, J Mol Biol. 1993 Dec 20;234(4):1084-93. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7903398 7903398]
<div style="clear:both"></div>
[[Category: Drosophila melanogaster]]
__TOC__
[[Category: Single protein]]
</StructureSection>
[[Category: Billeter, M.]]
[[Category: Drosophila subobscura]]
[[Category: Gehring, W J.]]
[[Category: Large Structures]]
[[Category: Muller, M.]]
[[Category: Billeter M]]
[[Category: Otting, G.]]
[[Category: Gehring WJ]]
[[Category: Qian, Y Q.]]
[[Category: Muller M]]
[[Category: Wuthrich, K.]]
[[Category: Otting G]]
[[Category: Dna binding protein/dna]]
[[Category: Qian YQ]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 10:16:27 2008''
[[Category: Wuthrich K]]

Latest revision as of 18:24, 13 March 2024

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

Structural highlights

1ahd is a 3 chain structure with sequence from Drosophila subobscura. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ANTP_DROSU Sequence-specific transcription factor which is part of a developmental regulatory system that regulates segmental identity in the mesothorax. Provides cells with specific positional identities on the anterior-posterior axis (By similarity).[UniProtKB:P02833]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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OCA
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