6t7d: Difference between revisions

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<StructureSection load='6t7d' size='340' side='right'caption='[[6t7d]], [[Resolution|resolution]] 4.40&Aring;' scene=''>
<StructureSection load='6t7d' size='340' side='right'caption='[[6t7d]], [[Resolution|resolution]] 4.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6t7d]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T7D OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6T7D FirstGlance]. <br>
<table><tr><td colspan='2'>[[6t7d]] is a 11 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=6T7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6T7D FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HIST2H3A, HIST2H3C, H3F2, H3FM, HIST2H3D ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H2AB, H2AFM, HIST1H2AE, H2AFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H2BK, H2BFT, HIRIP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), SOX11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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]] 4.4&#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=6t7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t7d OCA], [http://pdbe.org/6t7d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t7d RCSB], [http://www.ebi.ac.uk/pdbsum/6t7d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t7d 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=6t7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t7d OCA], [https://pdbe.org/6t7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6t7d RCSB], [https://www.ebi.ac.uk/pdbsum/6t7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6t7d ProSAT]</span></td></tr>
</table>
</table>
== Disease ==
[[http://www.uniprot.org/uniprot/SOX11_HUMAN SOX11_HUMAN]] Coffin-Siris syndrome. The disease is caused by mutations affecting the gene represented in this entry.
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/H2B1K_HUMAN H2B1K_HUMAN]] 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.  Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid. [[http://www.uniprot.org/uniprot/SOX11_HUMAN SOX11_HUMAN]] Transcription factor that acts as a transcriptional activator (PubMed:24886874). Binds cooperatively with POU3F2/BRN2 or POU3F1/OCT6 to gene promoters, which enhances transcriptional activation (By similarity). Acts as a transcriptional activator of TEAD2 by binding to its gene promoter and first intron (By similarity). Plays a redundant role with SOX4 and SOX12 in cell survival of developing tissues such as the neural tube, branchial arches and somites, thereby contributing to organogenesis (By similarity).[UniProtKB:Q7M6Y2]<ref>PMID:24886874</ref> 
[https://www.uniprot.org/uniprot/H32_HUMAN H32_HUMAN]  
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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</div>
</div>
<div class="pdbe-citations 6t7d" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 6t7d" style="background-color:#fffaf0;"></div>
==See Also==
*[[Histone 3D structures|Histone 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cramer, P]]
[[Category: Synthetic construct]]
[[Category: Dienemann, C]]
[[Category: Cramer P]]
[[Category: Dodonova, S O]]
[[Category: Dienemann C]]
[[Category: Taipale, J]]
[[Category: Dodonova SO]]
[[Category: Zhu, F]]
[[Category: Taipale J]]
[[Category: Dna]]
[[Category: Zhu F]]
[[Category: Histone]]
[[Category: Nuclear protein]]
[[Category: Nucleosome]]
[[Category: Pioneer factor]]
[[Category: Sox11]]
[[Category: Transcription factor]]

Latest revision as of 13:17, 22 May 2024

Structure of human Sox11 transcription factor in complex with a nucleosomeStructure of human Sox11 transcription factor in complex with a nucleosome

Structural highlights

6t7d is a 11 chain structure with sequence from Homo sapiens and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Electron Microscopy, Resolution 4.4Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

H32_HUMAN

Publication Abstract from PubMed

'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming(1,2). Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells(3). Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription.

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function.,Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer P Nature. 2020 Apr;580(7805):669-672. doi: 10.1038/s41586-020-2195-y. Epub 2020 Apr, 22. PMID:32350470[1]

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

See Also

References

  1. ↑ Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer P. Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Nature. 2020 Apr;580(7805):669-672. doi: 10.1038/s41586-020-2195-y. Epub 2020 Apr, 22. PMID:32350470 doi:http://dx.doi.org/10.1038/s41586-020-2195-y

6t7d, resolution 4.40Å

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