6iy2: Difference between revisions

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 <SX load='6iy2' size='340' side='right' viewer='molstar' caption='[[6iy2]], [[Resolution|resolution]] 3.47&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6iy2]] is a 11 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IY2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6IY2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6iy2]] is a 11 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus], [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C] and [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IY2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IY2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.47&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6iy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iy2 OCA], [http://pdbe.org/6iy2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iy2 RCSB], [http://www.ebi.ac.uk/pdbsum/6iy2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iy2 ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></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=6iy2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iy2 OCA], [https://pdbe.org/6iy2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6iy2 RCSB], [https://www.ebi.ac.uk/pdbsum/6iy2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6iy2 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SNF2_YEAST SNF2_YEAST]] Involved in transcriptional activation. Catalytic component of the SWI/SNF complex, an ATP-dependent chromatin-remodeling complex, which is required for the positive and negative regulation of gene expression of a large number of genes. It changes chromatin structure by altering DNA-histone contacts within a nucleosome, leading eventually to a change in nucleosome position, thus facilitating or repressing binding of gene-specific transcription factors. [[http://www.uniprot.org/uniprot/H4_XENLA H4_XENLA]] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.
+[https://www.uniprot.org/uniprot/H32_XENLA H32_XENLA] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Chromatin remodellers include diverse enzymes with distinct biological functions, but nucleosome-sliding activity appears to be a common theme(1,2). Among the remodelling enzymes, Snf2 serves as the prototype to study the action of this protein family. Snf2 and related enzymes share two conserved RecA-like lobes(3), which by themselves are able to couple ATP hydrolysis to chromatin remodelling. The mechanism by which these enzymes couple ATP hydrolysis to translocate the nucleosome along the DNA remains unclear(2,4-8). Here we report the structures of Saccharomyces cerevisiae Snf2 bound to the nucleosome in the presence of ADP and ADP-BeFx. Snf2 in the ADP-bound state adopts an open conformation similar to that in the apo state, and induces a one-base-pair DNA bulge at superhelix location 2 (SHL2), with the tracking strand showing greater distortion than the guide strand. The DNA distortion propagates to the proximal end, leading to staggered translocation of the two strands. The binding of ADP-BeFx triggers a closed conformation of the enzyme, resetting the nucleosome to a relaxed state. Snf2 shows altered interactions with the DNA in different nucleotide states, providing the structural basis for DNA translocation. Together, our findings suggest a fundamental mechanism for the DNA translocation that underlies chromatin remodelling.
-Mechanism of DNA translocation underlying chromatin remodelling by Snf2.,Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z Nature. 2019 Mar;567(7748):409-413. doi: 10.1038/s41586-019-1029-2. Epub 2019 Mar, 13. PMID:30867599<ref>PMID:30867599</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6iy2" style="background-color:#fffaf0;"></div>
 ==See Also==
+*[[Helicase 3D structures|Helicase 3D structures]]
 *[[Histone 3D structures|Histone 3D structures]]
-== References ==
-<references/>
 __TOC__
 </SX>
 [[Category: Large Structures]]
-[[Category: Chen, Z]]
+[[Category: Mus musculus]]
-[[Category: Li, M]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Li, X]]
+[[Category: Xenopus laevis]]
-[[Category: Liu, X]]
+[[Category: Chen Z]]
-[[Category: Xia, X]]
+[[Category: Li M]]
-[[Category: Chromatin remodeling]]
+[[Category: Li X]]
-[[Category: Complex]]
+[[Category: Liu X]]
-[[Category: Dna binding protein]]
+[[Category: Xia X]]
-[[Category: Gene regulation]]
-[[Category: Nucleosome]]
-[[Category: Structural protein-hydrolase-dna complex]]