6z2j - Revision history

OCA at 10:22, 22 May 2024

OCA — Wed, 22 May 2024 10:22:49 GMT

←Older revision		Revision as of 10:22, 22 May 2024
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	<StructureSection load='6z2j' size='340' side='right'caption='[[6z2j]], [[Resolution\|resolution]] 4.00Å' scene=''>		<StructureSection load='6z2j' size='340' side='right'caption='[[6z2j]], [[Resolution\|resolution]] 4.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6z2j]] is a 6 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=6Z2J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6Z2J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6z2j]] is a 6 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=6Z2J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z2J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=IHP:INOSITOL+HEXAKISPHOSPHATE'>IHP</scene>~~, ~~<scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 4Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>HDAC1, RPD3L1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN]), DNTTIP1, C20orf167, TDIF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN]), MIDEAS, C14orf117, C14orf43, ELMSAN1 ([http~~:~~//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IHP:INOSITOL+HEXAKISPHOSPHATE'>IHP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98]~~ </~~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=6z2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z2j OCA], [https://pdbe.org/6z2j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z2j RCSB], [https://www.ebi.ac.uk/pdbsum/6z2j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z2j ProSAT]</span></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=6z2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z2j OCA], [~~http~~://pdbe.org/6z2j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6z2j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6z2j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6z2j ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HDAC1_HUMAN HDAC1_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Deacetylates SP proteins, SP1 and SP3, and regulates their function. Component of the BRG1-RB1-HDAC1 complex, which negatively regulates the CREST-mediated transcription in resting neurons. Upon calcium stimulation, HDAC1 is released from the complex and CREBBP is recruited, which facilitates transcriptional activation. Deacetylates TSHZ3 and regulates its transcriptional repressor activity. Deacetylates 'Lys-310' in RELA and thereby inhibits the transcriptional activity of NF-kappa-B. Component a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development.<ref>PMID:12837748</ref> <ref>PMID:16478997</ref> <ref>PMID:17000776</ref> <ref>PMID:17704056</ref> <ref>PMID:19081374</ref> <ref>PMID:19343227</ref> [[http://www.uniprot.org/uniprot/TDIF1_HUMAN TDIF1_HUMAN]] Shown to enhance TdT activity, in vitro. Also acts as a transcriptional regulator, binding to the consensus sequence 5'-GNTGCATG-3' following an AT-tract. Associates with RAB20 promoter and positively regulates its transcription.<ref>PMID:11473582</ref> <ref>PMID:23874396</ref>	+	[https://www.uniprot.org/uniprot/HDAC1_HUMAN HDAC1_HUMAN] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Deacetylates SP proteins, SP1 and SP3, and regulates their function. Component of the BRG1-RB1-HDAC1 complex, which negatively regulates the CREST-mediated transcription in resting neurons. Upon calcium stimulation, HDAC1 is released from the complex and CREBBP is recruited, which facilitates transcriptional activation. Deacetylates TSHZ3 and regulates its transcriptional repressor activity. Deacetylates 'Lys-310' in RELA and thereby inhibits the transcriptional activity of NF-kappa-B. Component a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development.<ref>PMID:12837748</ref> <ref>PMID:16478997</ref> <ref>PMID:17000776</ref> <ref>PMID:17704056</ref> <ref>PMID:19081374</ref> <ref>PMID:19343227</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Histone deacetylase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fairall, L]]	+	[[Category: Fairall L]]
-	[[Category: Millard~~, C J~~]]	+	[[Category: Millard CJ]]
-	[[Category: Ragan~~, T J~~]]	+	[[Category: Ragan TJ]]
-	[[Category: Saleh, A]]	+	[[Category: Saleh A]]
-	[[Category: Savva~~, C G~~]]	+	[[Category: Savva CG]]
-	[[Category: Schwabe~~, J W.R]]~~	+	[[Category: Schwabe JWR]]
-	~~[[Category: Gene regulation]]~~	+
-	~~[[Category: Hdac1 mideas elmsan1 dnttip1 tdif1 histone deacetylase midac~~]]	+

OCA at 06:41, 7 October 2020

OCA — Wed, 07 Oct 2020 06:41:53 GMT

←Older revision		Revision as of 06:41, 7 October 2020
Line 1:		Line 1:

	==The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex==		==The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex==
-	<StructureSection load='6z2j' size='340' side='right'caption='[[6z2j]]' scene=''>	+	<StructureSection load='6z2j' size='340' side='right'caption='[[6z2j]], [[Resolution\|resolution]] 4.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z2J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Z2J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6z2j]] is a 6 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=6Z2J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Z2J 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=6z2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z2j OCA], [http://pdbe.org/6z2j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6z2j RCSB], [http://www.ebi.ac.uk/pdbsum/6z2j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6z2j ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IHP:INOSITOL+HEXAKISPHOSPHATE'>IHP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HDAC1, RPD3L1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), DNTTIP1, C20orf167, TDIF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), MIDEAS, C14orf117, C14orf43, ELMSAN1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </span></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=6z2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z2j OCA], [http://pdbe.org/6z2j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6z2j RCSB], [http://www.ebi.ac.uk/pdbsum/6z2j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6z2j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HDAC1_HUMAN HDAC1_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Deacetylates SP proteins, SP1 and SP3, and regulates their function. Component of the BRG1-RB1-HDAC1 complex, which negatively regulates the CREST-mediated transcription in resting neurons. Upon calcium stimulation, HDAC1 is released from the complex and CREBBP is recruited, which facilitates transcriptional activation. Deacetylates TSHZ3 and regulates its transcriptional repressor activity. Deacetylates 'Lys-310' in RELA and thereby inhibits the transcriptional activity of NF-kappa-B. Component a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development.<ref>PMID:12837748</ref> <ref>PMID:16478997</ref> <ref>PMID:17000776</ref> <ref>PMID:17704056</ref> <ref>PMID:19081374</ref> <ref>PMID:19343227</ref> [[http://www.uniprot.org/uniprot/TDIF1_HUMAN TDIF1_HUMAN]] Shown to enhance TdT activity, in vitro. Also acts as a transcriptional regulator, binding to the consensus sequence 5'-GNTGCATG-3' following an AT-tract. Associates with RAB20 promoter and positively regulates its transcription.<ref>PMID:11473582</ref> <ref>PMID:23874396</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	MiDAC is one of seven distinct, large multi-protein complexes that recruit class I histone deacetylases to the genome to regulate gene expression. Despite implications of involvement in cell cycle regulation and in several cancers, surprisingly little is known about the function or structure of MiDAC. Here we show that MiDAC is important for chromosome alignment during mitosis in cancer cell lines. Mice lacking the MiDAC proteins, DNTTIP1 or MIDEAS, die with identical phenotypes during late embryogenesis due to perturbations in gene expression that result in heart malformation and haematopoietic failure. This suggests that MiDAC has an essential and unique function that cannot be compensated by other HDAC complexes. Consistent with this, the cryoEM structure of MiDAC reveals a unique and distinctive mode of assembly. Four copies of HDAC1 are positioned at the periphery with outward-facing active sites suggesting that the complex may target multiple nucleosomes implying a processive deacetylase function.
		+
		+	The MiDAC histone deacetylase complex is essential for embryonic development and has a unique multivalent structure.,Turnbull RE, Fairall L, Saleh A, Kelsall E, Morris KL, Ragan TJ, Savva CG, Chandru A, Millard CJ, Makarova OV, Smith CJ, Roseman AM, Fry AM, Cowley SM, Schwabe JWR Nat Commun. 2020 Jun 26;11(1):3252. doi: 10.1038/s41467-020-17078-8. PMID:32591534<ref>PMID:32591534</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6z2j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone deacetylase 3D structures\|Histone deacetylase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Histone deacetylase]]
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fairall L]]	+	[[Category: Fairall, L]]
-	[[Category: Millard CJ]]	+	[[Category: Millard, C J]]
-	[[Category: Ragan TJ]]	+	[[Category: Ragan, T J]]
-	[[Category: Saleh A]]	+	[[Category: Saleh, A]]
-	[[Category: Savva CG]]	+	[[Category: Savva, C G]]
-	[[Category: Schwabe ~~JWR~~]]	+	[[Category: Schwabe, J W.R]]
		+	[[Category: Gene regulation]]
		+	[[Category: Hdac1 mideas elmsan1 dnttip1 tdif1 histone deacetylase midac]]

OCA at 14:12, 8 July 2020

OCA — Wed, 08 Jul 2020 14:12:33 GMT

←Older revision		Revision as of 14:12, 8 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 6z2j is ~~ON HOLD until Paper Publication~~	+	==The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex==
-		+	<StructureSection load='6z2j' size='340' side='right'caption='[[6z2j]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z2J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Z2J FirstGlance]. <br>
-	~~Description~~:	+	</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=6z2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z2j OCA], [http://pdbe.org/6z2j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6z2j RCSB], [http://www.ebi.ac.uk/pdbsum/6z2j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6z2j ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Fairall L]]
		+	[[Category: Millard CJ]]
		+	[[Category: Ragan TJ]]
		+	[[Category: Saleh A]]
		+	[[Category: Savva CG]]
		+	[[Category: Schwabe JWR]]

OCA: Protected "6z2j" [edit=sysop:move=sysop]

OCA — Wed, 27 May 2020 05:03:15 GMT

Protected "6z2j" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:03, 27 May 2020

OCA: New page: '''Unreleased structure''' The entry 6z2j is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 May 2020 05:03:14 GMT

New page: '''Unreleased structure''' The entry 6z2j is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6z2j is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]