5pwd - Revision history

OCA at 14:22, 24 January 2024

OCA — Wed, 24 Jan 2024 14:22:34 GMT

←Older revision		Revision as of 14:22, 24 January 2024
Line 1:		Line 1:

	==PanDDA analysis group deposition -- Crystal Structure of SP100 in complex with N09600b==		==PanDDA analysis group deposition -- Crystal Structure of SP100 in complex with N09600b==
-	<StructureSection load='5pwd' size='340' side='right' caption='[[5pwd]], [[Resolution\|resolution]] 1.57Å' scene=''>	+	<StructureSection load='5pwd' size='340' side='right'caption='[[5pwd]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5pwd]] 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=5PWD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5PWD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5pwd]] 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=5PWD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PWD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=81P:4-(METHYLAMINO)BENZOIC+ACID'>81P</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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]] 1.569Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SP100 ([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=81P:4-(METHYLAMINO)BENZOIC+ACID'>81P</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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=5pwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pwd OCA], [~~http~~://pdbe.org/5pwd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5pwd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5pwd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5pwd 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=5pwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pwd OCA], [https://pdbe.org/5pwd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pwd RCSB], [https://www.ebi.ac.uk/pdbsum/5pwd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pwd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~SP100_HUMAN SP100_HUMAN~~]] Together with PML, this tumor suppressor is a major constituent of the PML bodies, a subnuclear organelle involved in a large number of physiological processes including cell growth, differentiation and apoptosis. Functions as a transcriptional coactivator of ETS1 and ETS2 according to PubMed:11909962. Under certain conditions, it may also act as a corepressor of ETS1 preventing its binding to DNA according to PubMed:15247905. Through the regulation of ETS1 it may play a role in angiogenesis, controlling endothelial cell motility and invasion. Through interaction with the MRN complex it may be involved in the regulation of telomeres lengthening. May also regulate TP53-mediated transcription and through CASP8AP2, regulate FAS-mediated apoptosis. Also plays a role in infection by viruses, including human cytomegalovirus and Epstein-Barr virus, through mechanisms that may involve chromatin and/or transcriptional regulation.<ref>PMID:11909962</ref> <ref>PMID:14647468</ref> <ref>PMID:15247905</ref> <ref>PMID:15592518</ref> <ref>PMID:15767676</ref> <ref>PMID:16177824</ref> <ref>PMID:17245429</ref> <ref>PMID:21274506</ref> <ref>PMID:21880768</ref>	+	[https://www.uniprot.org/uniprot/H0Y4R8_HUMAN H0Y4R8_HUMAN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: Arrowsmith~~, C H~~]]	+	[[Category: Large Structures]]
-	[[Category: Bountra, C]]	+	[[Category: Arrowsmith CH]]
-	[[Category: Bradley~~, A R~~]]	+	[[Category: Bountra C]]
-	[[Category: Brandao-Neto, J]]	+	[[Category: Bradley AR]]
-	[[Category: Brennan~~, P E~~]]	+	[[Category: Brandao-Neto J]]
-	[[Category: Collins, P]]	+	[[Category: Brennan PE]]
-	[[Category: Cox, O]]	+	[[Category: Collins P]]
-	~~[[Category: Delft, F von~~]]	+	[[Category: Cox O]]
-	[[Category: Dias, A]]	+	[[Category: Dias A]]
-	[[Category: Douangamath, A]]	+	[[Category: Douangamath A]]
-	[[Category: Edwards, A]]	+	[[Category: Edwards A]]
-	[[Category: Fairhead, M]]	+	[[Category: Fairhead M]]
-	[[Category: Krojer, T]]	+	[[Category: Krojer T]]
-	[[Category: MacLean, E]]	+	[[Category: MacLean E]]
-	[[Category: Ng, J]]	+	[[Category: Ng J]]
-	[[Category: Pearce~~, N M~~]]	+	[[Category: Pearce NM]]
-	[[Category: Renjie, Z]]	+	[[Category: Renjie Z]]
-	[[Category: Sethi, R]]	+	[[Category: Sethi R]]
-	[[Category: Talon, R]]	+	[[Category: Talon R]]
-	[[Category: Wright, N]]	+	[[Category: Wright N]]
-	[[Category: ~~Bromodomain]]~~	+	[[Category: Von Delft F]]
-	~~[[Category: Epigenetic]]~~	+
-	~~[[Category: Pandda]]~~	+
-	~~[[Category: Sgc - diamond i04-1 fragment screening]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Xchemexplorer~~]]	+

OCA at 14:15, 6 November 2017

OCA — Mon, 06 Nov 2017 14:15:56 GMT

←Older revision		Revision as of 14:15, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5pwd' size='340' side='right' caption='[[5pwd]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='5pwd' size='340' side='right' caption='[[5pwd]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5pwd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PWD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5pwd]] 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=5PWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PWD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=81P:4-(METHYLAMINO)BENZOIC+ACID'>81P</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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"><scene name='pdbligand=81P:4-(METHYLAMINO)BENZOIC+ACID'>81P</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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">SP100 ([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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5pwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pwd OCA], [http://pdbe.org/5pwd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pwd RCSB], [http://www.ebi.ac.uk/pdbsum/5pwd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pwd ProSAT]</span></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=5pwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pwd OCA], [http://pdbe.org/5pwd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pwd RCSB], [http://www.ebi.ac.uk/pdbsum/5pwd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pwd ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Bountra, C]]		[[Category: Bountra, C]]

OCA at 09:23, 27 September 2017

OCA — Wed, 27 Sep 2017 09:23:45 GMT

←Older revision		Revision as of 09:23, 27 September 2017
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SP100_HUMAN SP100_HUMAN]] Together with PML, this tumor suppressor is a major constituent of the PML bodies, a subnuclear organelle involved in a large number of physiological processes including cell growth, differentiation and apoptosis. Functions as a transcriptional coactivator of ETS1 and ETS2 according to PubMed:11909962. Under certain conditions, it may also act as a corepressor of ETS1 preventing its binding to DNA according to PubMed:15247905. Through the regulation of ETS1 it may play a role in angiogenesis, controlling endothelial cell motility and invasion. Through interaction with the MRN complex it may be involved in the regulation of telomeres lengthening. May also regulate TP53-mediated transcription and through CASP8AP2, regulate FAS-mediated apoptosis. Also plays a role in infection by viruses, including human cytomegalovirus and Epstein-Barr virus, through mechanisms that may involve chromatin and/or transcriptional regulation.<ref>PMID:11909962</ref> <ref>PMID:14647468</ref> <ref>PMID:15247905</ref> <ref>PMID:15592518</ref> <ref>PMID:15767676</ref> <ref>PMID:16177824</ref> <ref>PMID:17245429</ref> <ref>PMID:21274506</ref> <ref>PMID:21880768</ref>		[[http://www.uniprot.org/uniprot/SP100_HUMAN SP100_HUMAN]] Together with PML, this tumor suppressor is a major constituent of the PML bodies, a subnuclear organelle involved in a large number of physiological processes including cell growth, differentiation and apoptosis. Functions as a transcriptional coactivator of ETS1 and ETS2 according to PubMed:11909962. Under certain conditions, it may also act as a corepressor of ETS1 preventing its binding to DNA according to PubMed:15247905. Through the regulation of ETS1 it may play a role in angiogenesis, controlling endothelial cell motility and invasion. Through interaction with the MRN complex it may be involved in the regulation of telomeres lengthening. May also regulate TP53-mediated transcription and through CASP8AP2, regulate FAS-mediated apoptosis. Also plays a role in infection by viruses, including human cytomegalovirus and Epstein-Barr virus, through mechanisms that may involve chromatin and/or transcriptional regulation.<ref>PMID:11909962</ref> <ref>PMID:14647468</ref> <ref>PMID:15247905</ref> <ref>PMID:15592518</ref> <ref>PMID:15767676</ref> <ref>PMID:16177824</ref> <ref>PMID:17245429</ref> <ref>PMID:21274506</ref> <ref>PMID:21880768</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In macromolecular crystallography, the rigorous detection of changed states (for example, ligand binding) is difficult unless signal is strong. Ambiguous ('weak' or 'noisy') density is experimentally common, since molecular states are generally only fractionally present in the crystal. Existing methodologies focus on generating maximally accurate maps whereby minor states become discernible; in practice, such map interpretation is disappointingly subjective, time-consuming and methodologically unsound. Here we report the PanDDA method, which automatically reveals clear electron density for the changed state-even from inaccurate maps-by subtracting a proportion of the confounding 'ground state'; changed states are objectively identified from statistical analysis of density distributions. The method is completely general, implying new best practice for all changed-state studies, including the routine collection of multiple ground-state crystals. More generally, these results demonstrate: the incompleteness of atomic models; that single data sets contain insufficient information to model them fully; and that accuracy requires further map-deconvolution approaches.
		+
		+	A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.,Pearce NM, Krojer T, Bradley AR, Collins P, Nowak RP, Talon R, Marsden BD, Kelm S, Shi J, Deane CM, von Delft F Nat Commun. 2017 Apr 24;8:15123. doi: 10.1038/ncomms15123. PMID:28436492<ref>PMID:28436492</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5pwd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:46, 15 March 2017

OCA — Wed, 15 Mar 2017 21:46:29 GMT

←Older revision		Revision as of 21:46, 15 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5pwd is ON HOLD~~	+	==PanDDA analysis group deposition -- Crystal Structure of SP100 in complex with N09600b==
-		+	<StructureSection load='5pwd' size='340' side='right' caption='[[5pwd]], [[Resolution\|resolution]] 1.57Å' scene=''>
-	~~Authors: Krojer, T.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5pwd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PWD FirstGlance]. <br>
-	~~Description:~~ PanDDA analysis group deposition --Crystal Structure of SP100 in complex with N09600b	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=81P:4-(METHYLAMINO)BENZOIC+ACID'>81P</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5pwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pwd OCA], [http://pdbe.org/5pwd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pwd RCSB], [http://www.ebi.ac.uk/pdbsum/5pwd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pwd ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SP100_HUMAN SP100_HUMAN]] Together with PML, this tumor suppressor is a major constituent of the PML bodies, a subnuclear organelle involved in a large number of physiological processes including cell growth, differentiation and apoptosis. Functions as a transcriptional coactivator of ETS1 and ETS2 according to PubMed:11909962. Under certain conditions, it may also act as a corepressor of ETS1 preventing its binding to DNA according to PubMed:15247905. Through the regulation of ETS1 it may play a role in angiogenesis, controlling endothelial cell motility and invasion. Through interaction with the MRN complex it may be involved in the regulation of telomeres lengthening. May also regulate TP53-mediated transcription and through CASP8AP2, regulate FAS-mediated apoptosis. Also plays a role in infection by viruses, including human cytomegalovirus and Epstein-Barr virus, through mechanisms that may involve chromatin and/or transcriptional regulation.<ref>PMID:11909962</ref> <ref>PMID:14647468</ref> <ref>PMID:15247905</ref> <ref>PMID:15592518</ref> <ref>PMID:15767676</ref> <ref>PMID:16177824</ref> <ref>PMID:17245429</ref> <ref>PMID:21274506</ref> <ref>PMID:21880768</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arrowsmith, C H]]
		+	[[Category: Bountra, C]]
		+	[[Category: Bradley, A R]]
		+	[[Category: Brandao-Neto, J]]
		+	[[Category: Brennan, P E]]
		+	[[Category: Collins, P]]
		+	[[Category: Cox, O]]
		+	[[Category: Delft, F von]]
		+	[[Category: Dias, A]]
		+	[[Category: Douangamath, A]]
		+	[[Category: Edwards, A]]
		+	[[Category: Fairhead, M]]
	[[Category: Krojer, T]]		[[Category: Krojer, T]]
		+	[[Category: MacLean, E]]
		+	[[Category: Ng, J]]
		+	[[Category: Pearce, N M]]
		+	[[Category: Renjie, Z]]
		+	[[Category: Sethi, R]]
		+	[[Category: Talon, R]]
		+	[[Category: Wright, N]]
		+	[[Category: Bromodomain]]
		+	[[Category: Epigenetic]]
		+	[[Category: Pandda]]
		+	[[Category: Sgc - diamond i04-1 fragment screening]]
		+	[[Category: Transcription]]
		+	[[Category: Xchemexplorer]]

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

OCA — Thu, 09 Mar 2017 13:10:19 GMT

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

←Older revision

Revision as of 13:10, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5pwd is ON HOLD Authors: Krojer, T. Description: PanDDA analysis group deposition --Crystal Structure of SP100 in complex with N09600b [[Category: ...

OCA — Thu, 09 Mar 2017 13:10:18 GMT

New page: '''Unreleased structure''' The entry 5pwd is ON HOLD Authors: Krojer, T. Description: PanDDA analysis group deposition --Crystal Structure of SP100 in complex with N09600b [[Category: ...

New page

'''Unreleased structure'''

The entry 5pwd is ON HOLD

Authors: Krojer, T.

Description: PanDDA analysis group deposition --Crystal Structure of SP100 in complex with N09600b
[[Category: Unreleased Structures]]
[[Category: Krojer, T]]