9r4i: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 9r4i is ~~ON HOLD until Paper~~ Publication

==An auto inhibitory loop in the MiDAC histone deacetylase complex==

== Structural highlights ==

<table><tr><td colspan='2'>[[9r4i]] 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=9R4I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9R4I FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.92Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9r4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9r4i OCA], [https://pdbe.org/9r4i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9r4i RCSB], [https://www.ebi.ac.uk/pdbsum/9r4i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9r4i ProSAT]</span></td></tr>

</table>

== Function ==

[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>

== Publication Abstract from PubMed ==

MIDEAS is a scaffold protein that, together with DNTTIP1, mediates assembly of the MiDAC histone deacetylase complex. Mice lacking MiDAC die before birth suggesting a key developmental function. Here, we report two unrelated individuals, with a multisystem disorder characterised by delayed speech development, joint contractures, dysmorphic features and dysmotility of the gut. Both individuals have the same de novo heterozygous missense variant in MIDEAS (p.Tyr654Ser). A cryoEM structure of the MiDAC complex reveals that this amino acid is located in a conserved auto-inhibitory loop that covers the active site of the deacetylase enzyme. We suggest that the variant results in loop displacement leading to elevated deacetylase activity. In support, we observe reciprocal gene expression changes in patient fibroblasts compared with a cell line following rapid MiDAC degradation. Our results establish MIDEAS as a dominant monogenic disease gene and that hyperactivity of the MiDAC complex results in a characteristic multisystem disorder.

~~Authors~~:

A de novo missense variant in MIDEAS results in increased deacetylase activity of the MiDAC HDAC complex causing a neurodevelopmental syndrome.,Fairall L, Sirvydis K, Turnbull RE, Knottnerus SJ, Gonchar O, Muskett FW, Jukes-Jones R, van Brussel L, van de Geer E, van Gassen K, Badenhorst P, Johnson D, Terhal PA, van Hasselt PM, van Jaarsveld RH, Schwabe JW Nat Commun. 2025 Nov 25;16(1):10472. doi: 10.1038/s41467-025-65472-x. PMID:41290615<ref>PMID:41290615</ref>

~~Description~~:

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

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Homo sapiens]]

[[Category: Large Structures]]

[[Category: Fairall L]]

[[Category: Schwabe JWR]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9r4i is ON HOLD  until Paper Publication
+==An auto inhibitory loop in the MiDAC histone deacetylase complex==
+<StructureSection load='9r4i' size='340' side='right'caption='[[9r4i]], [[Resolution|resolution]] 2.92&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9r4i]] 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=9R4I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9R4I FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.92&#8491;</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9r4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9r4i OCA], [https://pdbe.org/9r4i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9r4i RCSB], [https://www.ebi.ac.uk/pdbsum/9r4i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9r4i ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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;">
+== Publication Abstract from PubMed ==
+MIDEAS is a scaffold protein that, together with DNTTIP1, mediates assembly of the MiDAC histone deacetylase complex. Mice lacking MiDAC die before birth suggesting a key developmental function. Here, we report two unrelated individuals, with a multisystem disorder characterised by delayed speech development, joint contractures, dysmorphic features and dysmotility of the gut. Both individuals have the same de novo heterozygous missense variant in MIDEAS (p.Tyr654Ser). A cryoEM structure of the MiDAC complex reveals that this amino acid is located in a conserved auto-inhibitory loop that covers the active site of the deacetylase enzyme. We suggest that the variant results in loop displacement leading to elevated deacetylase activity. In support, we observe reciprocal gene expression changes in patient fibroblasts compared with a cell line following rapid MiDAC degradation. Our results establish MIDEAS as a dominant monogenic disease gene and that hyperactivity of the MiDAC complex results in a characteristic multisystem disorder.
-Authors:
+A de novo missense variant in MIDEAS results in increased deacetylase activity of the MiDAC HDAC complex causing a neurodevelopmental syndrome.,Fairall L, Sirvydis K, Turnbull RE, Knottnerus SJ, Gonchar O, Muskett FW, Jukes-Jones R, van Brussel L, van de Geer E, van Gassen K, Badenhorst P, Johnson D, Terhal PA, van Hasselt PM, van Jaarsveld RH, Schwabe JW Nat Commun. 2025 Nov 25;16(1):10472. doi: 10.1038/s41467-025-65472-x. PMID:41290615<ref>PMID:41290615</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 9r4i" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Fairall L]]
+[[Category: Schwabe JWR]]