6r25 - Revision history

OCA at 05:16, 11 April 2020

OCA — Sat, 11 Apr 2020 05:16:14 GMT

←Older revision		Revision as of 05:16, 11 April 2020
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	<SX load='6r25' size='340' side='right' viewer='molstar' caption='[[6r25]], [[Resolution\|resolution]] 4.61Å' scene=''>		<SX load='6r25' size='340' side='right' viewer='molstar' caption='[[6r25]], [[Resolution\|resolution]] 4.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r25]] is a 13 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R25 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R25 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r25]] is a 13 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R25 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6R25 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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=6r25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r25 OCA], [http://pdbe.org/6r25 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r25 RCSB], [http://www.ebi.ac.uk/pdbsum/6r25 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r25 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=6r25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r25 OCA], [http://pdbe.org/6r25 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r25 RCSB], [http://www.ebi.ac.uk/pdbsum/6r25 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r25 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 23:58, 6 March 2020

OCA — Fri, 06 Mar 2020 23:58:57 GMT

←Older revision		Revision as of 23:58, 6 March 2020
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	==Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3==		==Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3==
-	<~~StructureSection~~ load='6r25' size='340' side='right'caption='[[6r25]], [[Resolution\|resolution]] 4.61Å' scene=''>	+	<SX load='6r25' size='340' side='right' viewer='molstar' caption='[[6r25]], [[Resolution\|resolution]] 4.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6r25]] is a 13 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R25 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6r25]] is a 13 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R25 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 6r25" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6r25" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone 3D structures\|Histone 3D structures]]
		+	*[[Lysine-specific histone demethylase 3D structures\|Lysine-specific histone demethylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chittori, S]]		[[Category: Chittori, S]]

OCA at 07:13, 24 April 2019

OCA — Wed, 24 Apr 2019 07:13:44 GMT

←Older revision		Revision as of 07:13, 24 April 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6r25 is ~~ON HOLD until Paper~~ Publication	+	==Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3==
		+	<StructureSection load='6r25' size='340' side='right'caption='[[6r25]], [[Resolution\|resolution]] 4.61Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6r25]] is a 13 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R25 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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=6r25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r25 OCA], [http://pdbe.org/6r25 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r25 RCSB], [http://www.ebi.ac.uk/pdbsum/6r25 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r25 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KDM1B_HUMAN KDM1B_HUMAN]] Histone demethylase that demethylates 'Lys-4' of histone H3, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Required for de novo DNA methylation of a subset of imprinted genes during oogenesis. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Demethylates both mono- and di-methylated 'Lys-4' of histone H3. Has no effect on tri-methylated 'Lys-4', mono-, di- or tri-methylated 'Lys-9', mono-, di- or tri-methylated 'Lys-27', mono-, di- or tri-methylated 'Lys-36' of histone H3, or on mono-, di- or tri-methylated 'Lys-20' of histone H4 (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	LSD1 and LSD2 are homologous histone demethylases with opposite biological outcomes related to chromatin silencing and transcription elongation, respectively. Unlike LSD1, LSD2 nucleosome-demethylase activity relies on a specific linker peptide from the multidomain protein NPAC. We used single-particle cryoelectron microscopy (cryo-EM), in combination with kinetic and mutational analysis, to analyze the mechanisms underlying the function of the human LSD2/NPAC-linker/nucleosome complex. Weak interactions between LSD2 and DNA enable multiple binding modes for the association of the demethylase to the nucleosome. The demethylase thereby captures mono- and dimethyl Lys4 of the H3 tail to afford histone demethylation. Our studies also establish that the dehydrogenase domain of NPAC serves as a catalytically inert oligomerization module. While LSD1/CoREST forms a nucleosome docking platform at silenced gene promoters, LSD2/NPAC is a multifunctional enzyme complex with flexible linkers, tailored for rapid chromatin modification, in conjunction with the advance of the RNA polymerase on actively transcribed genes.

-	~~Authors: Marabelli~~, C., ~~Pilotto~~, S., Chittori, S., ~~Subramaniam~~, S., Mattevi, A.	+	A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.,Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A Cell Rep. 2019 Apr 9;27(2):387-399.e7. doi: 10.1016/j.celrep.2019.03.061. PMID:30970244<ref>PMID:30970244</ref>

-	~~Description: Structure~~ of ~~LSD2~~/~~NPAC~~-~~linker/nucleosome core particle complex~~: ~~Class 3~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Subramaniam, S~~]]	+	<div class="pdbe-citations 6r25" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Chittori, S]]		[[Category: Chittori, S]]
	[[Category: Marabelli, C]]		[[Category: Marabelli, C]]
	[[Category: Mattevi, A]]		[[Category: Mattevi, A]]
	[[Category: Pilotto, S]]		[[Category: Pilotto, S]]
		+	[[Category: Subramaniam, S]]
		+	[[Category: Chromatin reader]]
		+	[[Category: Epigenetic]]
		+	[[Category: Evolution of protein function]]
		+	[[Category: Flavoenzyme]]
		+	[[Category: Gene regulation]]
		+	[[Category: Histone demethylation]]
		+	[[Category: Molecular recognition]]

OCA at 04:52, 3 April 2019

OCA — Wed, 03 Apr 2019 04:52:54 GMT

←Older revision		Revision as of 04:52, 3 April 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6r25 is ON HOLD	+	The entry 6r25 is ON HOLD until Paper Publication

	Authors: Marabelli, C., Pilotto, S., Chittori, S., Subramaniam, S., Mattevi, A.		Authors: Marabelli, C., Pilotto, S., Chittori, S., Subramaniam, S., Mattevi, A.

OCA: Protected "6r25" [edit=sysop:move=sysop]

OCA — Wed, 27 Mar 2019 05:11:57 GMT

Protected "6r25" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:11, 27 March 2019

OCA: New page: '''Unreleased structure''' The entry 6r25 is ON HOLD Authors: Marabelli, C., Pilotto, S., Chittori, S., Subramaniam, S., Mattevi, A. Description: Structure of LSD2/NPAC-linker/nucleoso...

OCA — Wed, 27 Mar 2019 05:11:55 GMT

New page: '''Unreleased structure''' The entry 6r25 is ON HOLD Authors: Marabelli, C., Pilotto, S., Chittori, S., Subramaniam, S., Mattevi, A. Description: Structure of LSD2/NPAC-linker/nucleoso...

New page

'''Unreleased structure'''

The entry 6r25 is ON HOLD

Authors: Marabelli, C., Pilotto, S., Chittori, S., Subramaniam, S., Mattevi, A.

Description: Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3
[[Category: Unreleased Structures]]
[[Category: Subramaniam, S]]
[[Category: Chittori, S]]
[[Category: Marabelli, C]]
[[Category: Mattevi, A]]
[[Category: Pilotto, S]]