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6luj

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Current revision (10:47, 27 March 2024) (edit) (undo)
 
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<StructureSection load='6luj' size='340' side='right'caption='[[6luj]], [[Resolution|resolution]] 1.12&Aring;' scene=''>
<StructureSection load='6luj' size='340' side='right'caption='[[6luj]], [[Resolution|resolution]] 1.12&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6luj]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LUJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LUJ FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6luj]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LUJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LUJ FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.12&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SAMD1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=SO4:SULFATE+ION'>SO4</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=6luj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6luj OCA], [https://pdbe.org/6luj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6luj RCSB], [https://www.ebi.ac.uk/pdbsum/6luj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6luj ProSAT]</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=6luj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6luj OCA], [https://pdbe.org/6luj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6luj RCSB], [https://www.ebi.ac.uk/pdbsum/6luj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6luj ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/SAMD1_HUMAN SAMD1_HUMAN]] May play a role in atherogenesis by immobilizing LDL in the atherial wall.<ref>PMID:16159594</ref>
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[https://www.uniprot.org/uniprot/SAMD1_HUMAN SAMD1_HUMAN] May play a role in atherogenesis by immobilizing LDL in the atherial wall.<ref>PMID:16159594</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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CpG islands (CGIs) are key regulatory DNA elements at most promoters, but how they influence the chromatin status and transcription remains elusive. Here, we identify and characterize SAMD1 (SAM domain-containing protein 1) as an unmethylated CGI-binding protein. SAMD1 has an atypical winged-helix domain that directly recognizes unmethylated CpG-containing DNA via simultaneous interactions with both the major and the minor groove. The SAM domain interacts with L3MBTL3, but it can also homopolymerize into a closed pentameric ring. At a genome-wide level, SAMD1 localizes to H3K4me3-decorated CGIs, where it acts as a repressor. SAMD1 tethers L3MBTL3 to chromatin and interacts with the KDM1A histone demethylase complex to modulate H3K4me2 and H3K4me3 levels at CGIs, thereby providing a mechanism for SAMD1-mediated transcriptional repression. The absence of SAMD1 impairs ES cell differentiation processes, leading to misregulation of key biological pathways. Together, our work establishes SAMD1 as a newly identified chromatin regulator acting at unmethylated CGIs.
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The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands.,Stielow B, Zhou Y, Cao Y, Simon C, Pogoda HM, Jiang J, Ren Y, Phanor SK, Rohner I, Nist A, Stiewe T, Hammerschmidt M, Shi Y, Bulyk ML, Wang Z, Liefke R Sci Adv. 2021 May 12;7(20). pii: 7/20/eabf2229. doi: 10.1126/sciadv.abf2229., Print 2021 May. PMID:33980486<ref>PMID:33980486</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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<div class="pdbe-citations 6luj" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Human]]
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[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Cao, Y]]
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[[Category: Cao Y]]
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[[Category: Wang, Z]]
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[[Category: Wang Z]]
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[[Category: Zhou, Y]]
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[[Category: Zhou Y]]
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[[Category: Cpg-island]]
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[[Category: Dna binding protein]]
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[[Category: Pentamer]]
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[[Category: Transcription]]
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Current revision

Crystal structure of the SAMD1 SAM domain

PDB ID 6luj

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