7s6m - Revision history

OCA at 16:45, 18 October 2023

OCA — Wed, 18 Oct 2023 16:45:37 GMT

←Older revision		Revision as of 16:45, 18 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7s6m]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7S6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7S6M FirstGlance]. <br>		<table><tr><td colspan='2'>[[7s6m]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7S6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7S6M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 3.2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[https://proteopedia.org/fgij/fg.htm?mol=7s6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s6m OCA], [https://pdbe.org/7s6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s6m RCSB], [https://www.ebi.ac.uk/pdbsum/7s6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s6m 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=7s6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s6m OCA], [https://pdbe.org/7s6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s6m RCSB], [https://www.ebi.ac.uk/pdbsum/7s6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s6m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PARP1_HUMAN PARP1_HUMAN]] Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.<ref>PMID:17177976</ref> <ref>PMID:18172500</ref> <ref>PMID:19344625</ref> <ref>PMID:19661379</ref>	+	[https://www.uniprot.org/uniprot/PARP1_HUMAN PARP1_HUMAN] Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.<ref>PMID:17177976</ref> <ref>PMID:18172500</ref> <ref>PMID:19344625</ref> <ref>PMID:19661379</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7s6m" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7s6m" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Poly(ADP-ribose) polymerase 3D structures\|Poly(ADP-ribose) polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:48, 7 September 2022

OCA — Wed, 07 Sep 2022 19:48:09 GMT

←Older revision		Revision as of 19:48, 7 September 2022
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	<StructureSection load='7s6m' size='340' side='right'caption='[[7s6m]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='7s6m' size='340' side='right'caption='[[7s6m]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7s6m]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7S6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7S6M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7s6m]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7S6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7S6M FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7s68\|7s68]], [[7s6h\|7s6h]], [[7s81\|7s81]]</div></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=7s6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s6m OCA], [https://pdbe.org/7s6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s6m RCSB], [https://www.ebi.ac.uk/pdbsum/7s6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s6m 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=7s6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s6m OCA], [https://pdbe.org/7s6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s6m RCSB], [https://www.ebi.ac.uk/pdbsum/7s6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s6m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PARP1_HUMAN PARP1_HUMAN]] Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.<ref>PMID:17177976</ref> <ref>PMID:18172500</ref> <ref>PMID:19344625</ref> <ref>PMID:19661379</ref>	+	[[https://www.uniprot.org/uniprot/PARP1_HUMAN PARP1_HUMAN]] Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.<ref>PMID:17177976</ref> <ref>PMID:18172500</ref> <ref>PMID:19344625</ref> <ref>PMID:19661379</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pascal, J M~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Rouleau-Turcotte, E~~]]	+	[[Category: Pascal JM]]
-	[[Category: ~~Adp~~-~~ribose transferase]]~~	+	[[Category: Rouleau-Turcotte E]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Dna break detection]]~~	+
-	~~[[Category: Parp]]~~	+
-	~~[[Category: Zinc finger~~]]	+

OCA at 07:11, 20 July 2022

OCA — Wed, 20 Jul 2022 07:11:11 GMT

←Older revision		Revision as of 07:11, 20 July 2022
Line 1:		Line 1:

	==Human PARP1 deltaV687-E688 bound to a DNA double strand break.==		==Human PARP1 deltaV687-E688 bound to a DNA double strand break.==
-	<StructureSection load='7s6m' size='340' side='right'caption='[[7s6m]]' scene=''>	+	<StructureSection load='7s6m' size='340' side='right'caption='[[7s6m]], [[Resolution\|resolution]] 3.20Å' 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=7S6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7S6M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7s6m]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7S6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7S6M FirstGlance]. <br>
-	</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=7s6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s6m OCA], [https://pdbe.org/7s6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s6m RCSB], [https://www.ebi.ac.uk/pdbsum/7s6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s6m 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7s68\|7s68]], [[7s6h\|7s6h]], [[7s81\|7s81]]</div></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=7s6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s6m OCA], [https://pdbe.org/7s6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s6m RCSB], [https://www.ebi.ac.uk/pdbsum/7s6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s6m ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/PARP1_HUMAN PARP1_HUMAN]] Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.<ref>PMID:17177976</ref> <ref>PMID:18172500</ref> <ref>PMID:19344625</ref> <ref>PMID:19661379</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	PARP1 rapidly detects DNA strand break damage and allosterically signals break detection to the PARP1 catalytic domain to activate poly(ADP-ribose) production from NAD(+). PARP1 activation is characterized by dynamic changes in the structure of a regulatory helical domain (HD); yet, there are limited insights into the specific contributions that the HD makes to PARP1 allostery. Here, we have determined crystal structures of PARP1 in isolated active states that display specific HD conformations. These captured snapshots and biochemical analysis illustrate HD contributions to PARP1 multi-domain and high-affinity interaction with DNA damage, provide novel insights into the mechanics of PARP1 allostery, and indicate how HD active conformations correspond to alterations in the catalytic region that reveal the active site to NAD(+). Our work deepens the understanding of PARP1 catalytic activation, the dynamics of the binding site of PARP inhibitor compounds, and the mechanisms regulating PARP1 retention on DNA damage.
		+
		+	Captured snapshots of PARP1 in the active state reveal the mechanics of PARP1 allostery.,Rouleau-Turcotte E, Krastev DB, Pettitt SJ, Lord CJ, Pascal JM Mol Cell. 2022 Jun 28. pii: S1097-2765(22)00570-6. doi:, 10.1016/j.molcel.2022.06.011. PMID:35793673<ref>PMID:35793673</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7s6m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Rouleau-Turcotte, E~~, Pascal, JM~~]]	+	[[Category: Pascal, J M]]
		+	[[Category: Rouleau-Turcotte, E]]
		+	[[Category: Adp-ribose transferase]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Dna break detection]]
		+	[[Category: Parp]]
		+	[[Category: Zinc finger]]

OCA at 07:27, 29 June 2022

OCA — Wed, 29 Jun 2022 07:27:04 GMT

←Older revision		Revision as of 07:27, 29 June 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7s6m is ON HOLD until Paper Publication~~	+	==Human PARP1 deltaV687-E688 bound to a DNA double strand break.==
-		+	<StructureSection load='7s6m' size='340' side='right'caption='[[7s6m]]' scene=''>
-	~~Authors: Rouleau-Turcotte, E., Pascal, J.M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7S6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7S6M FirstGlance]. <br>
-	~~Description:~~ Human PARP1 deltaV687-E688 bound to a DNA double strand break.	+	</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=7s6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s6m OCA], [https://pdbe.org/7s6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s6m RCSB], [https://www.ebi.ac.uk/pdbsum/7s6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s6m ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Pascal~~, J.M]]	+	__TOC__
-	[[Category: Rouleau-Turcotte, E]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Rouleau-Turcotte, E, Pascal, JM]]

OCA at 07:45, 29 September 2021

OCA — Wed, 29 Sep 2021 07:45:41 GMT

←Older revision		Revision as of 07:45, 29 September 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7s6m is ON HOLD	+	The entry 7s6m is ON HOLD until Paper Publication

	Authors: Rouleau-Turcotte, E., Pascal, J.M.		Authors: Rouleau-Turcotte, E., Pascal, J.M.

OCA: Protected "7s6m" [edit=sysop:move=sysop]

OCA — Wed, 22 Sep 2021 05:40:14 GMT

Protected "7s6m" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:40, 22 September 2021

OCA: New page: '''Unreleased structure''' The entry 7s6m is ON HOLD Authors: Rouleau-Turcotte, E., Pascal, J.M. Description: Human PARP1 deltaV687-E688 bound to a DNA double strand break. [[Category:...

OCA — Wed, 22 Sep 2021 05:40:13 GMT

New page: '''Unreleased structure''' The entry 7s6m is ON HOLD Authors: Rouleau-Turcotte, E., Pascal, J.M. Description: Human PARP1 deltaV687-E688 bound to a DNA double strand break. [[Category:...

New page

'''Unreleased structure'''

The entry 7s6m is ON HOLD

Authors: Rouleau-Turcotte, E., Pascal, J.M.

Description: Human PARP1 deltaV687-E688 bound to a DNA double strand break.
[[Category: Unreleased Structures]]
[[Category: Pascal, J.M]]
[[Category: Rouleau-Turcotte, E]]