2ky8: Difference between revisions

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 ==Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target methylated DNA sequence==
-<StructureSection load='2ky8' size='340' side='right' caption='[[2ky8]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2ky8' size='340' side='right'caption='[[2ky8]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ky8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KY8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KY8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ky8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KY8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=TED:5-[(1E)-14-CARBOXY-10,13-BIS(CARBOXYMETHYL)-3,8-DIOXO-4,7,10,13-TETRAAZATETRADEC-1-EN-1-YL]-2-DEOXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>TED</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TED:5-[(1E)-14-CARBOXY-10,13-BIS(CARBOXYMETHYL)-3,8-DIOXO-4,7,10,13-TETRAAZATETRADEC-1-EN-1-YL]-2-DEOXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>TED</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3c2i|3c2i]], [[1ig4|1ig4]]</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=2ky8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ky8 OCA], [https://pdbe.org/2ky8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ky8 RCSB], [https://www.ebi.ac.uk/pdbsum/2ky8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ky8 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MBD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9031 CHICK])</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=2ky8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ky8 OCA], [http://pdbe.org/2ky8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ky8 RCSB], [http://www.ebi.ac.uk/pdbsum/2ky8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ky8 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/Q5EFL0_CHICK Q5EFL0_CHICK]
-The epigenetic code of DNA methylation is interpreted chiefly by methyl cytosine binding domain (MBD) proteins which in turn recruit multiprotein co-repressor complexes. We previously isolated one such complex, MBD2-NuRD, from primary erythroid cells and have shown it contributes to embryonic/fetal beta-type globin gene silencing during development. This complex has been implicated in silencing tumor suppressor genes in a variety of human tumor cell types. Here we present structural details of chicken MBD2 bound to a methylated DNA sequence from the rho-globin promoter to which it binds in vivo and mediates developmental transcriptional silencing in normal erythroid cells. While previous studies have failed to show sequence specificity for MBD2 outside of the symmetric mCpG, we find that this domain binds in a single orientation on the rho-globin target DNA sequence. Further, we show that the orientation and affinity depends on guanine immediately following the mCpG dinucleotide. Dynamic analyses show that DNA binding stabilizes the central beta-sheet, while the N- and C-terminal regions of the protein maintain mobility. Taken together, these data lead to a model in which DNA binding stabilizes the MBD2 structure and that binding orientation and affinity is influenced by the DNA sequence surrounding the central mCpG.
-Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target-methylated DNA sequence.,Scarsdale JN, Webb HD, Ginder GD, Williams DC Jr Nucleic Acids Res. 2011 Apr 29. PMID:21531701<ref>PMID:21531701</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2ky8" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Methyl CpG binding protein|Methyl CpG binding protein]]
+*[[Methyl CpG binding protein 3D structures|Methyl CpG binding protein 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Chick]]
+[[Category: Gallus gallus]]
-[[Category: Scarsdale, J N]]
+[[Category: Large Structures]]
-[[Category: Williams, D C]]
+[[Category: Scarsdale Jr JN]]
-[[Category: Dna binding domain]]
+[[Category: Williams Jr DC]]
-[[Category: Transcription-dna complex]]