2kae

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{{Seed}}
 
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[[Image:2kae.png|left|200px]]
 
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==data-driven model of MED1:DNA complex==
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The line below this paragraph, containing "STRUCTURE_2kae", creates the "Structure Box" on the page.
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<StructureSection load='2kae' size='340' side='right'caption='[[2kae]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2kae]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KAE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KAE FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_2kae| PDB=2kae | SCENE= }}
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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=2kae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kae OCA], [https://pdbe.org/2kae PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kae RCSB], [https://www.ebi.ac.uk/pdbsum/2kae PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kae ProSAT]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ka/2kae_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2kae ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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MED-1 is a member of a group of divergent GATA-type zinc finger proteins recently identified in several species of Caenorhabditis. The med genes are transcriptional regulators that are involved in the specification of the mesoderm and endoderm precursor cells in nematodes. Unlike other GATA-type zinc fingers that recognize the consensus sequence (A/C/T)GATA(A/G), the MED-1 zinc finger (MED1zf) binds the larger and atypical site GTATACT(TC)(3). We have examined the basis for this unusual DNA specificity using a range of biochemical and biophysical approaches. Most strikingly, we show that although the core of the MED1zf structure is similar to that of GATA-1, the basic tail C-terminal to the zinc finger unexpectedly adopts an a-helical structure upon binding DNA. This additional helix appears to contact the major groove of the DNA, making contacts that explain the extended DNA consensus sequence observed for MED1zf. Our data expand the versatility of DNA recognition by GATA-type zinc fingers and perhaps shed new light on the DNA-binding properties of mammalian GATA factors.
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===data-driven model of MED1:DNA complex===
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Structural analysis of med-1 reveals unexpected diversity in the mechanism of DNA recognition by gata-type zinc finger domains.,Lowry JA, Gamsjaeger R, Thong SY, Hung W, Kwan AH, Broitman-Maduro G, Matthews JM, Maduro M, Mackay JP J Biol Chem. 2008 Dec 18. PMID:19095651<ref>PMID:19095651</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_19095651}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2kae" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19095651 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19095651}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2KAE is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KAE OCA].
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==Reference==
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Structural analysis of med-1 reveals unexpected diversity in the mechanism of DNA recognition by gata-type zinc finger domains., Lowry JA, Gamsjaeger R, Thong SY, Hung W, Kwan AH, Broitman-Maduro G, Matthews JM, Maduro M, Mackay JP, J Biol Chem. 2008 Dec 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19095651 19095651]
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[[Category: Caenorhabditis elegans]]
[[Category: Caenorhabditis elegans]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
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[[Category: Broitman-Maduro G]]
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[[Category: Dna]]
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[[Category: Gamsjaeger R]]
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[[Category: Gata-type]]
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[[Category: Hung W]]
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[[Category: Metal-binding]]
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[[Category: Kwan AH]]
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[[Category: Transcription factor]]
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[[Category: Lowry JA]]
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[[Category: Transcription/dna complex]]
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[[Category: Mackay JP]]
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[[Category: Zinc]]
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[[Category: Maduro M]]
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[[Category: Zinc finger]]
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[[Category: Matthews JM]]
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[[Category: Zinc-finger]]
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[[Category: Thong S]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 11 20:18:56 2009''
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Current revision

data-driven model of MED1:DNA complex

PDB ID 2kae

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