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2kae

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data-driven model of MED1:DNA complex

Structural highlights

2kae is a 3 chain structure with sequence from Caenorhabditis elegans. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

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

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Lowry JA, Gamsjaeger R, Thong SY, Hung W, Kwan AH, Broitman-Maduro G, Matthews JM, Maduro M, Mackay JP. Structural analysis of med-1 reveals unexpected diversity in the mechanism of DNA recognition by gata-type zinc finger domains. J Biol Chem. 2008 Dec 18. PMID:19095651 doi:M808712200

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2kae"

@@ Line 1: / Line 1: @@
 ==data-driven model of MED1:DNA complex==
-<StructureSection load='2kae' size='340' side='right' caption='[[2kae]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
+<StructureSection load='2kae' size='340' side='right'caption='[[2kae]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2kae]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Caeel Caeel]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KAE FirstGlance]. <br>
+<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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">med-1, T24D3.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL])</td></tr>
+<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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2kae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kae OCA], [http://pdbe.org/2kae PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kae RCSB], [http://www.ebi.ac.uk/pdbsum/2kae PDBsum]</span></td></tr>
+<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>
 </table>
 == Evolutionary Conservation ==
@@ Line 11: / Line 12: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ka/2kae_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ka/2kae_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 31: @@
 __TOC__
 </StructureSection>
-[[Category: Caeel]]
+[[Category: Caenorhabditis elegans]]
-[[Category: Broitman-Maduro, G]]
+[[Category: Large Structures]]
-[[Category: Gamsjaeger, R]]
+[[Category: Broitman-Maduro G]]
-[[Category: Hung, W]]
+[[Category: Gamsjaeger R]]
-[[Category: Kwan, A H]]
+[[Category: Hung W]]
-[[Category: Lowry, J A]]
+[[Category: Kwan AH]]
-[[Category: Mackay, J P]]
+[[Category: Lowry JA]]
-[[Category: Maduro, M]]
+[[Category: Mackay JP]]
-[[Category: Matthews, J M]]
+[[Category: Maduro M]]
-[[Category: Thong, S]]
+[[Category: Matthews JM]]
-[[Category: Dna]]
+[[Category: Thong S]]
-[[Category: Gata-type]]
-[[Category: Metal-binding]]
-[[Category: Transcription factor]]
-[[Category: Transcription-dna complex]]
-[[Category: Zinc finger]]
-[[Category: Zinc-finger]]

2kae

From Proteopedia

Current revision

data-driven model of MED1:DNA complex

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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