5dkd - Revision history

OCA at 21:46, 28 June 2023

2023-06-28T21:46:01Z

← Older revision		Revision as of 21:46, 28 June 2023
Line 3:		Line 3:
	<StructureSection load='5dkd' size='340' side='right'caption='[[5dkd]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5dkd' size='340' side='right'caption='[[5dkd]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5dkd]] is a 2 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=5DKD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5DKD FirstGlance]. <br>		<table><tr><td colspan='2'>[[5dkd]] is a 2 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=5DKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DKD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5BW:(2E)-1-(2-HYDROXYPHENYL)-3-[(1R,4R)-5-(PYRIDIN-2-YL)-2,5-DIAZABICYCLO[2.2.1]HEPT-2-YL]PROP-2-EN-1-ONE'>5BW</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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">X-ray diffraction, [[Resolution\|Resolution]] 2Å</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 ([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=5BW:(2E)-1-(2-HYDROXYPHENYL)-3-[(1R,4R)-5-(PYRIDIN-2-YL)-2,5-DIAZABICYCLO[2.2.1]HEPT-2-YL]PROP-2-EN-1-ONE'>5BW</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dkd OCA], [~~http~~://pdbe.org/5dkd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dkd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dkd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dkd 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=5dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dkd OCA], [https://pdbe.org/5dkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dkd RCSB], [https://www.ebi.ac.uk/pdbsum/5dkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dkd ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
	[~~[http~~://www.uniprot.org/uniprot/SMCA4_HUMAN SMCA4_HUMAN]] Defects in SMARCA4 are the cause of rhabdoid tumor predisposition syndrome type 2 (RTPS2) [MIM:[~~http~~://omim.org/entry/613325 613325]]. RTPS2 is a familial cancer syndrome predisposing to renal or extrarenal malignant rhabdoid tumors and to a variety of tumors of the central nervous system, including choroid plexus carcinoma, medulloblastoma, and central primitive neuroectodermal tumors. Rhabdoid tumors are the most aggressive and lethal malignancies occurring in early childhood.<ref>PMID:20137775</ref> Defects in SMARCA4 are the cause of mental retardation autosomal dominant type 16 (MRD16) [MIM:[~~http~~://omim.org/entry/614609 614609]]. A disease characterized by multiple congenital anomalies and mental retardation. Mental retardation is defined by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period. MRD16 patients manifest developmental delay, absent or hypoplastic fifth fingernails or toenails, thick eyebrows and long eyelashes, hirsutism. Additional findings include hypotonia, microcephaly, seizures, a Dandy-Walker malformation, and vision and hearing problems.<ref>PMID:22426308</ref>		[https://www.uniprot.org/uniprot/SMCA4_HUMAN SMCA4_HUMAN] Defects in SMARCA4 are the cause of rhabdoid tumor predisposition syndrome type 2 (RTPS2) [MIM:[https://omim.org/entry/613325 613325]. RTPS2 is a familial cancer syndrome predisposing to renal or extrarenal malignant rhabdoid tumors and to a variety of tumors of the central nervous system, including choroid plexus carcinoma, medulloblastoma, and central primitive neuroectodermal tumors. Rhabdoid tumors are the most aggressive and lethal malignancies occurring in early childhood.<ref>PMID:20137775</ref> Defects in SMARCA4 are the cause of mental retardation autosomal dominant type 16 (MRD16) [MIM:[https://omim.org/entry/614609 614609]. A disease characterized by multiple congenital anomalies and mental retardation. Mental retardation is defined by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period. MRD16 patients manifest developmental delay, absent or hypoplastic fifth fingernails or toenails, thick eyebrows and long eyelashes, hirsutism. Additional findings include hypotonia, microcephaly, seizures, a Dandy-Walker malformation, and vision and hearing problems.<ref>PMID:22426308</ref>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/SMCA4_HUMAN SMCA4_HUMAN]] Transcriptional coactivator cooperating with nuclear hormone receptors to potentiate transcriptional activation. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth. SMARCA4/BAF190A may promote neural stem cell self-renewal/proliferation by enhancing Notch-dependent proliferative signals, while concurrently making the neural stem cell insensitive to SHH-dependent differentiating cues (By similarity). Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene. Acts as a corepressor of ZEB1 to regulate E-cadherin transcription and is required for induction of epithelial-mesenchymal transition (EMT) by ZEB1.<ref>PMID:12837248</ref> <ref>PMID:19571879</ref> <ref>PMID:20418909</ref>		[https://www.uniprot.org/uniprot/SMCA4_HUMAN SMCA4_HUMAN] Transcriptional coactivator cooperating with nuclear hormone receptors to potentiate transcriptional activation. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth. SMARCA4/BAF190A may promote neural stem cell self-renewal/proliferation by enhancing Notch-dependent proliferative signals, while concurrently making the neural stem cell insensitive to SHH-dependent differentiating cues (By similarity). Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene. Acts as a corepressor of ZEB1 to regulate E-cadherin transcription and is required for induction of epithelial-mesenchymal transition (EMT) by ZEB1.<ref>PMID:12837248</ref> <ref>PMID:19571879</ref> <ref>PMID:20418909</ref>

	==See Also==		==See Also==
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Arrowsmith~~, C H~~]]		[[Category: Arrowsmith CH]]
	[[Category: Bountra, C]]		[[Category: Bountra C]]
	[[Category: Burgess-Brown, N]]		[[Category: Burgess-Brown N]]
	~~[[Category: Delft, F von~~]]		[[Category: Edwards AM]]
	[[Category: Edwards~~, A M~~]]		[[Category: Fedorov O]]
	[[Category: Fedorov, O]]		[[Category: Filippakopoulos P]]
	[[Category: Filippakopoulos, P]]		[[Category: Gerstenberger BS]]
	[[Category: Gerstenberger~~, B S~~]]		[[Category: Knapp S]]
	[[Category: Knapp, S]]		[[Category: Muller S]]
	[[Category: Muller, S]]		[[Category: Newman JA]]
	[[Category: Newman~~, J A~~]]		[[Category: Nunez-Alonso G]]
	[[Category: Nunez-Alonso, G]]		[[Category: Owen DR]]
	[[Category: Owen~~, D R~~]]		[[Category: Savitsky P]]
	[[Category: Savitsky, P]]		[[Category: Tallant C]]
	[[Category: Tallant, C]]		[[Category: Von Delft F]]
	[[Category: ~~Chromatin remodeling]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Swi-snf complex]]~~
	~~[[Category: Transcription~~]]

OCA at 08:08, 8 April 2020

2020-04-08T08:08:02Z

← Older revision		Revision as of 08:08, 8 April 2020
Line 1:		Line 1:

	==Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe==		==Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe==
	<StructureSection load='5dkd' size='340' side='right' caption='[[5dkd]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5dkd' size='340' side='right'caption='[[5dkd]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5dkd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DKD OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DKD FirstGlance]. <br>		<table><tr><td colspan='2'>[[5dkd]] is a 2 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=5DKD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DKD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BW:(2E)-1-(2-HYDROXYPHENYL)-3-[(1R,4R)-5-(PYRIDIN-2-YL)-2,5-DIAZABICYCLO[2.2.1]HEPT-2-YL]PROP-2-EN-1-ONE'>5BW</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5BW:(2E)-1-(2-HYDROXYPHENYL)-3-[(1R,4R)-5-(PYRIDIN-2-YL)-2,5-DIAZABICYCLO[2.2.1]HEPT-2-YL]PROP-2-EN-1-ONE'>5BW</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dkd OCA], [http://pdbe.org/5dkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dkd RCSB], [http://www.ebi.ac.uk/pdbsum/5dkd PDBsum]</span></td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dkd OCA], [http://pdbe.org/5dkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dkd RCSB], [http://www.ebi.ac.uk/pdbsum/5dkd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dkd ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 10:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SMCA4_HUMAN SMCA4_HUMAN]] Transcriptional coactivator cooperating with nuclear hormone receptors to potentiate transcriptional activation. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth. SMARCA4/BAF190A may promote neural stem cell self-renewal/proliferation by enhancing Notch-dependent proliferative signals, while concurrently making the neural stem cell insensitive to SHH-dependent differentiating cues (By similarity). Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene. Acts as a corepressor of ZEB1 to regulate E-cadherin transcription and is required for induction of epithelial-mesenchymal transition (EMT) by ZEB1.<ref>PMID:12837248</ref> <ref>PMID:19571879</ref> <ref>PMID:20418909</ref>		[[http://www.uniprot.org/uniprot/SMCA4_HUMAN SMCA4_HUMAN]] Transcriptional coactivator cooperating with nuclear hormone receptors to potentiate transcriptional activation. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth. SMARCA4/BAF190A may promote neural stem cell self-renewal/proliferation by enhancing Notch-dependent proliferative signals, while concurrently making the neural stem cell insensitive to SHH-dependent differentiating cues (By similarity). Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene. Acts as a corepressor of ZEB1 to regulate E-cadherin transcription and is required for induction of epithelial-mesenchymal transition (EMT) by ZEB1.<ref>PMID:12837248</ref> <ref>PMID:19571879</ref> <ref>PMID:20418909</ref>

			==See Also==
			*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Bountra, C]]		[[Category: Bountra, C]]

OCA at 04:09, 16 October 2015

2015-10-16T04:09:23Z

← Older revision		Revision as of 04:09, 16 October 2015
Line 1:		Line 1:
	'''~~Unreleased structure~~'''		==Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe==
			<StructureSection load='5dkd' size='340' side='right' caption='[[5dkd]], [[Resolution\|resolution]] 2.00Å' scene=''>
	~~The entry~~ 5dkd is ~~ON HOLD~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[5dkd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DKD FirstGlance]. <br>
	~~Authors~~: ~~Tallant~~, C., ~~Owen~~, D.R., ~~Gerstenberger, B~~.S., ~~Fedorov~~, O., ~~Savitsky~~, P., ~~Nunez-Alonso~~, G.~~, Newman, J~~.A., ~~Filippakopoulos~~, P., ~~Burgess~~-~~Brown~~, N., ~~von Delft~~, F., ~~Arrowsmith~~, C.H., ~~Edwards, A~~.M.~~, Bountra, C~~.~~, Muller, S~~., ~~Knapp~~, S.		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BW:(2E)-1-(2-HYDROXYPHENYL)-3-[(1R,4R)-5-(PYRIDIN-2-YL)-2,5-DIAZABICYCLO[2.2.1]HEPT-2-YL]PROP-2-EN-1-ONE'>5BW</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dkd OCA], [http://pdbe.org/5dkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dkd RCSB], [http://www.ebi.ac.uk/pdbsum/5dkd PDBsum]</span></td></tr>
	~~Description: Crystal structure~~ of the ~~bromodomain~~ of ~~human BRG1~~ (~~SMARCA4~~) in complex ~~with PFI~~-~~3 chemical probe~~		</table>
	~~[[Category: Unreleased Structures]]~~		== Disease ==
	[[Category: ~~Gerstenberger~~, ~~B.S~~]]		[[http://www.uniprot.org/uniprot/SMCA4_HUMAN SMCA4_HUMAN]] Defects in SMARCA4 are the cause of rhabdoid tumor predisposition syndrome type 2 (RTPS2) [MIM:[http://omim.org/entry/613325 613325]]. RTPS2 is a familial cancer syndrome predisposing to renal or extrarenal malignant rhabdoid tumors and to a variety of tumors of the central nervous system, including choroid plexus carcinoma, medulloblastoma, and central primitive neuroectodermal tumors. Rhabdoid tumors are the most aggressive and lethal malignancies occurring in early childhood.<ref>PMID:20137775</ref> Defects in SMARCA4 are the cause of mental retardation autosomal dominant type 16 (MRD16) [MIM:[http://omim.org/entry/614609 614609]]. A disease characterized by multiple congenital anomalies and mental retardation. Mental retardation is defined by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period. MRD16 patients manifest developmental delay, absent or hypoplastic fifth fingernails or toenails, thick eyebrows and long eyelashes, hirsutism. Additional findings include hypotonia, microcephaly, seizures, a Dandy-Walker malformation, and vision and hearing problems.<ref>PMID:22426308</ref>
	[[Category: ~~Owen~~, ~~D.R~~]]		== Function ==
			[[http://www.uniprot.org/uniprot/SMCA4_HUMAN SMCA4_HUMAN]] Transcriptional coactivator cooperating with nuclear hormone receptors to potentiate transcriptional activation. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth. SMARCA4/BAF190A may promote neural stem cell self-renewal/proliferation by enhancing Notch-dependent proliferative signals, while concurrently making the neural stem cell insensitive to SHH-dependent differentiating cues (By similarity). Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene. Acts as a corepressor of ZEB1 to regulate E-cadherin transcription and is required for induction of epithelial-mesenchymal transition (EMT) by ZEB1.<ref>PMID:12837248</ref> <ref>PMID:19571879</ref> <ref>PMID:20418909</ref>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Arrowsmith, C H]]
			[[Category: Bountra, C]]
	[[Category: Burgess-Brown, N]]		[[Category: Burgess-Brown, N]]
	[[Category: ~~Nunez-Alonso~~, G]]		[[Category: Delft, F von]]
			[[Category: Edwards, A M]]
	[[Category: Fedorov, O]]		[[Category: Fedorov, O]]
			[[Category: Filippakopoulos, P]]
			[[Category: Gerstenberger, B S]]
			[[Category: Knapp, S]]
	[[Category: Muller, S]]		[[Category: Muller, S]]
	[[Category: ~~Knapp~~, ~~S]]~~		[[Category: Newman, J A]]
	~~[[Category: Bountra, C~~]]		[[Category: Nunez-Alonso, G]]
	[[Category: ~~Arrowsmith~~, ~~C.H~~]]		[[Category: Owen, D R]]
	[[Category: ~~Von Delft~~, F]]		[[Category: Savitsky, P]]
	[[Category: ~~Filippakopoulos~~, P]]
	~~[[Category: Edwards, A.M]]~~
	~~[[Category: Newman, J.A~~]]
	[[Category: Tallant, C]]		[[Category: Tallant, C]]
	[[Category: ~~Savitsky, P~~]]		[[Category: Chromatin remodeling]]
			[[Category: Hydrolase]]
			[[Category: Swi-snf complex]]
			[[Category: Transcription]]

OCA: Protected "5dkd" [edit=sysop:move=sysop]

2015-09-09T10:21:00Z

Protected "5dkd" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:21, 9 September 2015
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5dkd is ON HOLD Authors: Tallant, C., Owen, D.R., Gerstenberger, B.S., Fedorov, O., Savitsky, P., Nunez-Alonso, G., Newman, J.A., Filippakopoulos, P...

2015-09-09T10:20:59Z

New page: '''Unreleased structure''' The entry 5dkd is ON HOLD Authors: Tallant, C., Owen, D.R., Gerstenberger, B.S., Fedorov, O., Savitsky, P., Nunez-Alonso, G., Newman, J.A., Filippakopoulos, P...

New page

'''Unreleased structure'''

The entry 5dkd is ON HOLD

Authors: Tallant, C., Owen, D.R., Gerstenberger, B.S., Fedorov, O., Savitsky, P., Nunez-Alonso, G., Newman, J.A., Filippakopoulos, P., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Muller, S., Knapp, S.

Description: Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe
[[Category: Unreleased Structures]]
[[Category: Gerstenberger, B.S]]
[[Category: Owen, D.R]]
[[Category: Burgess-Brown, N]]
[[Category: Nunez-Alonso, G]]
[[Category: Fedorov, O]]
[[Category: Muller, S]]
[[Category: Knapp, S]]
[[Category: Bountra, C]]
[[Category: Arrowsmith, C.H]]
[[Category: Von Delft, F]]
[[Category: Filippakopoulos, P]]
[[Category: Edwards, A.M]]
[[Category: Newman, J.A]]
[[Category: Tallant, C]]
[[Category: Savitsky, P]]