4z5t

From Proteopedia

(Difference between revisions)

Revision as of 07:40, 10 May 2023

The nucleosome containing human H3.5

Structural highlights

4z5t is a 10 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

H3C_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. Hominid-specific H3.5/H3F3C preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes.^[1]

Publication Abstract from PubMed

BACKGROUND: Human histone H3.5 is a non-allelic H3 variant evolutionally derived from H3.3. The H3.5 mRNA is highly expressed in human testis. However, the function of H3.5 has remained poorly understood. RESULTS: We found that the H3.5 nucleosome is less stable than the H3.3 nucleosome. The crystal structure of the H3.5 nucleosome showed that the H3.5-specific Leu103 residue, which corresponds to the H3.3 Phe104 residue, reduces the hydrophobic interaction with histone H4. Mutational analyses revealed that the H3.5-specific Leu103 residue is responsible for the instability of the H3.5 nucleosome, both in vitro and in living cells. The H3.5 protein was present in human seminiferous tubules, but little to none was found in mature sperm. A chromatin immunoprecipitation coupled with sequencing analysis revealed that H3.5 accumulated around transcription start sites (TSSs) in testicular cells. CONCLUSIONS: We performed comprehensive studies of H3.5, and found the instability of the H3.5 nucleosome and the accumulation of H3.5 protein around TSSs in human testis. The unstable H3.5 nucleosome may function in the chromatin dynamics around the TSSs, during spermatogenesis.

Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis.,Urahama T, Harada A, Maehara K, Horikoshi N, Sato K, Sato Y, Shiraishi K, Sugino N, Osakabe A, Tachiwana H, Kagawa W, Kimura H, Ohkawa Y, Kurumizaka H Epigenetics Chromatin. 2016 Jan 15;9:2. doi: 10.1186/s13072-016-0051-y., eCollection 2016. PMID:26779285^[2]

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

References

↑ Schenk R, Jenke A, Zilbauer M, Wirth S, Postberg J. H3.5 is a novel hominid-specific histone H3 variant that is specifically expressed in the seminiferous tubules of human testes. Chromosoma. 2011 Jun;120(3):275-85. doi: 10.1007/s00412-011-0310-4. Epub 2011 Jan, 28. PMID:21274551 doi:10.1007/s00412-011-0310-4
↑ Urahama T, Harada A, Maehara K, Horikoshi N, Sato K, Sato Y, Shiraishi K, Sugino N, Osakabe A, Tachiwana H, Kagawa W, Kimura H, Ohkawa Y, Kurumizaka H. Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis. Epigenetics Chromatin. 2016 Jan 15;9:2. doi: 10.1186/s13072-016-0051-y., eCollection 2016. PMID:26779285 doi:http://dx.doi.org/10.1186/s13072-016-0051-y

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4z5t"

@@ Line 3: / Line 3: @@
 <StructureSection load='4z5t' size='340' side='right'caption='[[4z5t]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4z5t]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z5T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z5T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4z5t]] is a 10 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=4Z5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z5T FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">H3F3C ([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]), HIST1H2BJ, H2BFR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+</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=4z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z5t OCA], [https://pdbe.org/4z5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z5t RCSB], [https://www.ebi.ac.uk/pdbsum/4z5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z5t ProSAT]</span></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=4z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z5t OCA], [http://pdbe.org/4z5t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z5t RCSB], [http://www.ebi.ac.uk/pdbsum/4z5t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4z5t ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/H2B1J_HUMAN H2B1J_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.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref>   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.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref>  [[http://www.uniprot.org/uniprot/H3C_HUMAN H3C_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. Hominid-specific H3.5/H3F3C preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes.<ref>PMID:21274551</ref>
+[https://www.uniprot.org/uniprot/H3C_HUMAN H3C_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. Hominid-specific H3.5/H3F3C preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes.<ref>PMID:21274551</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Harada, A]]
+[[Category: Harada A]]
-[[Category: Horikoshi, N]]
+[[Category: Horikoshi N]]
-[[Category: Kagawa, W]]
+[[Category: Kagawa W]]
-[[Category: Kimura, H]]
+[[Category: Kimura H]]
-[[Category: Kurumizaka, H]]
+[[Category: Kurumizaka H]]
-[[Category: Maehara, K]]
+[[Category: Maehara K]]
-[[Category: Ohkawa, Y]]
+[[Category: Ohkawa Y]]
-[[Category: Osakabe, A]]
+[[Category: Osakabe A]]
-[[Category: Sato, K]]
+[[Category: Sato K]]
-[[Category: Sato, Y]]
+[[Category: Sato Y]]
-[[Category: Shiraishi, K]]
+[[Category: Shiraishi K]]
-[[Category: Sugino, N]]
+[[Category: Sugino N]]
-[[Category: Tachiwana, H]]
+[[Category: Tachiwana H]]
-[[Category: Urahama, T]]
+[[Category: Urahama T]]
-[[Category: Dna binding]]
-[[Category: Histone fold]]
-[[Category: Nucleus]]
-[[Category: Spermatogenesis]]
-[[Category: Structural protein-dna complex]]

4z5t

From Proteopedia

Revision as of 07:40, 10 May 2023

The nucleosome containing human H3.5

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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