6t93: Difference between revisions

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==Nucleosome with OCT4-SOX2 motif at SHL-6==

== Structural highlights ==

<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T93 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6T93 FirstGlance]. <br>

<table><tr><td colspan='2'>[[6t93]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6T93 FirstGlance]. <br>

</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=6t93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t93 OCA], [~~http~~://pdbe.org/6t93 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6t93 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6t93 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6t93 ProSAT]</span></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]] 3.49Å</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=6t93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t93 OCA], [https://pdbe.org/6t93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6t93 RCSB], [https://www.ebi.ac.uk/pdbsum/6t93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6t93 ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/H31_HUMAN H31_HUMAN]

== Publication Abstract from PubMed ==

Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs we focused on the reprogramming factors OCT4 and SOX2. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling cryo-EM structure determination at two preferred positions. Depending on motif location, OCT4-SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from Histone H2A/Histone H3 (H2A/H3); however, at an inverted motif, the TFs only induce local DNA distortions. OCT4 uses one of its two DNA binding domains to engage DNA in both structures, reading-out a partial motif. These findings explain site specific nucleosome engagement by the pluripotency factors OCT4-SOX2 and reveal how TFs distort nucleosomes to access chromatinized motifs.

Mechanisms of OCT4-SOX2 motif readout on nucleosomes.,Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schubeler D, Thoma NH Science. 2020 Apr 23. pii: science.abb0074. doi: 10.1126/science.abb0074. PMID:32327602<ref>PMID:32327602</ref>

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

</div>

==See Also==

*[[Histone 3D structures|Histone 3D structures]]

*[[OCT4 and SOX2 transcription factors|OCT4 and SOX2 transcription factors]]

== References ==

__TOC__

</StructureSection>

[[Category: Homo sapiens]]

[[Category: Large Structures]]

[[Category: Synthetic construct]]

[[Category: Bunker RD]]

[[Category: Cavadini S]]

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@@ Line 1: / Line 1: @@
 ==Nucleosome with OCT4-SOX2 motif at SHL-6==
-<StructureSection load='6t93' size='340' side='right'caption='[[6t93]]' scene=''>
+<StructureSection load='6t93' size='340' side='right'caption='[[6t93]], [[Resolution|resolution]] 3.49&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T93 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6T93 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6t93]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6T93 FirstGlance]. <br>
-</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=6t93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t93 OCA], [http://pdbe.org/6t93 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t93 RCSB], [http://www.ebi.ac.uk/pdbsum/6t93 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t93 ProSAT]</span></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]] 3.49&#8491;</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=6t93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t93 OCA], [https://pdbe.org/6t93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6t93 RCSB], [https://www.ebi.ac.uk/pdbsum/6t93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6t93 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/H31_HUMAN H31_HUMAN]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs we focused on the reprogramming factors OCT4 and SOX2. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling cryo-EM structure determination at two preferred positions. Depending on motif location, OCT4-SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from Histone H2A/Histone H3 (H2A/H3); however, at an inverted motif, the TFs only induce local DNA distortions. OCT4 uses one of its two DNA binding domains to engage DNA in both structures, reading-out a partial motif. These findings explain site specific nucleosome engagement by the pluripotency factors OCT4-SOX2 and reveal how TFs distort nucleosomes to access chromatinized motifs.
+Mechanisms of OCT4-SOX2 motif readout on nucleosomes.,Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schubeler D, Thoma NH Science. 2020 Apr 23. pii: science.abb0074. doi: 10.1126/science.abb0074. PMID:32327602<ref>PMID:32327602</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6t93" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Histone 3D structures|Histone 3D structures]]
+*[[OCT4 and SOX2 transcription factors|OCT4 and SOX2 transcription factors]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
+[[Category: Synthetic construct]]
 [[Category: Bunker RD]]
 [[Category: Cavadini S]]