3els - Revision history

OCA at 09:48, 21 February 2024

OCA — Wed, 21 Feb 2024 09:48:14 GMT

←Older revision		Revision as of 09:48, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3els' size='340' side='right'caption='[[3els]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3els' size='340' side='right'caption='[[3els]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3els]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ELS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ELS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3els]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ELS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ELS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3elv\|3elv]]~~</~~div~~><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">PML1, YLR016C, L1591 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])~~</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=3els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3els OCA], [https://pdbe.org/3els PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3els RCSB], [https://www.ebi.ac.uk/pdbsum/3els PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3els 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=3els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3els OCA], [https://pdbe.org/3els PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3els RCSB], [https://www.ebi.ac.uk/pdbsum/3els PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3els ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PML1_YEAST PML1_YEAST]] Required for efficient splicing and pre-mRNA nuclear retention.<ref>PMID:15565172</ref>	+	[https://www.uniprot.org/uniprot/PML1_YEAST PML1_YEAST] Required for efficient splicing and pre-mRNA nuclear retention.<ref>PMID:15565172</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3els ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3els ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The precursor mRNA retention and splicing (RES) complex mediates nuclear retention and enhances splicing of precursor mRNAs. The RES complex from yeast comprises three proteins, Snu17p, Bud13p and Pml1p. Snu17p acts as a central platform that concomitantly binds the Bud13p and Pml1p subunits via short peptide epitopes. As a step to decipher the molecular architecture of the RES complex, we have determined crystal structures of full-length Pml1p and N-terminally truncated Pml1p. The first 50 residues of full-length Pml1p, encompassing the Snu17p-binding region, are disordered, showing that Pml1p binds to Snu17p via an intrinsically unstructured region. The remainder of Pml1p folds as a forkhead-associated (FHA) domain, which is expanded by a number of noncanonical elements compared with known FHA domains from other proteins. An atypical N-terminal appendix runs across one beta-sheet and thereby stabilizes the domain as shown by deletion experiments. FHA domains are thought to constitute phosphopeptide-binding elements. Consistently, a sulfate ion was found at the putative phosphopeptide-binding loops of full-length Pml1p. The N-terminally truncated version of the protein lacked a similar phosphopeptide mimic but retained an almost identical structure. A long loop neighboring the putative phosphopeptide-binding site was disordered in both structures. Comparison with other FHA domain proteins suggests that this loop adopts a defined conformation upon ligand binding and thereby confers ligand specificity. Our results show that in the RES complex, an FHA domain of Pml1p is flexibly tethered via an unstructured N-terminal region to Snu17p.
-
-	Crystal structure of the Pml1p subunit of the yeast precursor mRNA retention and splicing complex.,Trowitzsch S, Weber G, Luhrmann R, Wahl MC J Mol Biol. 2009 Jan 16;385(2):531-41. Epub 2008 Nov 7. PMID:19010333<ref>PMID:19010333</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3els" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Luehrmann, R]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Trowitzsch, S]]	+	[[Category: Luehrmann R]]
-	[[Category: Wahl~~, M C~~]]	+	[[Category: Trowitzsch S]]
-	[[Category: Weber, G]]	+	[[Category: Wahl MC]]
-	~~[[Category: Intrinsically unstructured domain]]~~	+	[[Category: Weber G]]
-	~~[[Category: Mrna processing]]~~	+
-	~~[[Category: Mrna splicing]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Pre-mrna retention and splicing]]~~	+
-	~~[[Category: Protein phosphorylation]]~~	+
-	~~[[Category: Res complex]]~~	+
-	~~[[Category: Splicing~~]]	+

OCA at 11:52, 16 February 2022

OCA — Wed, 16 Feb 2022 11:52:53 GMT

←Older revision		Revision as of 11:52, 16 February 2022
Line 1:		Line 1:

	==Crystal Structure of Yeast Pml1p, Residues 51-204==		==Crystal Structure of Yeast Pml1p, Residues 51-204==
-	<StructureSection load='3els' size='340' side='right' caption='[[3els]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='3els' size='340' side='right'caption='[[3els]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3els]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ELS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ELS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3els]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ELS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ELS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3elv\|3elv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3elv\|3elv]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PML1, YLR016C, L1591 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PML1, YLR016C, L1591 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=3els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3els OCA], [~~http~~://pdbe.org/3els PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3els RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3els PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3els 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=3els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3els OCA], [https://pdbe.org/3els PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3els RCSB], [https://www.ebi.ac.uk/pdbsum/3els PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3els ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PML1_YEAST PML1_YEAST]] Required for efficient splicing and pre-mRNA nuclear retention.<ref>PMID:15565172</ref>	+	[[https://www.uniprot.org/uniprot/PML1_YEAST PML1_YEAST]] Required for efficient splicing and pre-mRNA nuclear retention.<ref>PMID:15565172</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Luehrmann, R]]		[[Category: Luehrmann, R]]
	[[Category: Trowitzsch, S]]		[[Category: Trowitzsch, S]]

OCA at 22:15, 2 December 2018

OCA — Sun, 02 Dec 2018 22:15:29 GMT

←Older revision		Revision as of 22:15, 2 December 2018
Line 1:		Line 1:
		+
	==Crystal Structure of Yeast Pml1p, Residues 51-204==		==Crystal Structure of Yeast Pml1p, Residues 51-204==
	<StructureSection load='3els' size='340' side='right' caption='[[3els]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3els' size='340' side='right' caption='[[3els]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3elv\|3elv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3elv\|3elv]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PML1, YLR016C, L1591 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PML1, YLR016C, L1591 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=3els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3els OCA], [http://pdbe.org/3els PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3els RCSB], [http://www.ebi.ac.uk/pdbsum/3els PDBsum]</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=3els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3els OCA], [http://pdbe.org/3els PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3els RCSB], [http://www.ebi.ac.uk/pdbsum/3els PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3els ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/el/3els_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/el/3els_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 17:50, 7 February 2016

OCA — Sun, 07 Feb 2016 17:50:56 GMT

←Older revision		Revision as of 17:50, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3els' size='340' side='right' caption='[[3els]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3els' size='340' side='right' caption='[[3els]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3els]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ELS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ELS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3els]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ELS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ELS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3elv\|3elv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3elv\|3elv]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PML1, YLR016C, L1591 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PML1, YLR016C, L1591 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=3els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3els OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3els RCSB], [http://www.ebi.ac.uk/pdbsum/3els PDBsum]</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=3els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3els OCA], [http://pdbe.org/3els PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3els RCSB], [http://www.ebi.ac.uk/pdbsum/3els PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3els ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3els" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: Luehrmann, R]]		[[Category: Luehrmann, R]]
	[[Category: Trowitzsch, S]]		[[Category: Trowitzsch, S]]

OCA at 17:13, 24 December 2014

OCA — Wed, 24 Dec 2014 17:13:02 GMT

←Older revision		Revision as of 17:13, 24 December 2014
Line 8:		Line 8:
	<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=3els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3els OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3els RCSB], [http://www.ebi.ac.uk/pdbsum/3els PDBsum]</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=3els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3els OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3els RCSB], [http://www.ebi.ac.uk/pdbsum/3els PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PML1_YEAST PML1_YEAST]] Required for efficient splicing and pre-mRNA nuclear retention.<ref>PMID:15565172</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 13:38, 19 November 2014

OCA — Wed, 19 Nov 2014 13:38:11 GMT

←Older revision		Revision as of 13:38, 19 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3els.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Yeast Pml1p, Residues 51-204==
		+	<StructureSection load='3els' size='340' side='right' caption='[[3els]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3els]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ELS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ELS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3elv\|3elv]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PML1, YLR016C, L1591 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=3els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3els OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3els RCSB], [http://www.ebi.ac.uk/pdbsum/3els PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/el/3els_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The precursor mRNA retention and splicing (RES) complex mediates nuclear retention and enhances splicing of precursor mRNAs. The RES complex from yeast comprises three proteins, Snu17p, Bud13p and Pml1p. Snu17p acts as a central platform that concomitantly binds the Bud13p and Pml1p subunits via short peptide epitopes. As a step to decipher the molecular architecture of the RES complex, we have determined crystal structures of full-length Pml1p and N-terminally truncated Pml1p. The first 50 residues of full-length Pml1p, encompassing the Snu17p-binding region, are disordered, showing that Pml1p binds to Snu17p via an intrinsically unstructured region. The remainder of Pml1p folds as a forkhead-associated (FHA) domain, which is expanded by a number of noncanonical elements compared with known FHA domains from other proteins. An atypical N-terminal appendix runs across one beta-sheet and thereby stabilizes the domain as shown by deletion experiments. FHA domains are thought to constitute phosphopeptide-binding elements. Consistently, a sulfate ion was found at the putative phosphopeptide-binding loops of full-length Pml1p. The N-terminally truncated version of the protein lacked a similar phosphopeptide mimic but retained an almost identical structure. A long loop neighboring the putative phosphopeptide-binding site was disordered in both structures. Comparison with other FHA domain proteins suggests that this loop adopts a defined conformation upon ligand binding and thereby confers ligand specificity. Our results show that in the RES complex, an FHA domain of Pml1p is flexibly tethered via an unstructured N-terminal region to Snu17p.

-	~~{{STRUCTURE_3els\| PDB=3els \| SCENE= }}~~	+	Crystal structure of the Pml1p subunit of the yeast precursor mRNA retention and splicing complex.,Trowitzsch S, Weber G, Luhrmann R, Wahl MC J Mol Biol. 2009 Jan 16;385(2):531-41. Epub 2008 Nov 7. PMID:19010333<ref>PMID:19010333</ref>

-	~~===Crystal Structure of Yeast Pml1p~~, ~~Residues 51-204===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19010333}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3els]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3ELS OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019010333<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Luehrmann, R.]]	+	[[Category: Luehrmann, R]]
-	[[Category: Trowitzsch, S.]]	+	[[Category: Trowitzsch, S]]
-	[[Category: Wahl, M C.]]	+	[[Category: Wahl, M C]]
-	[[Category: Weber, G.]]	+	[[Category: Weber, G]]
	[[Category: Intrinsically unstructured domain]]		[[Category: Intrinsically unstructured domain]]
	[[Category: Mrna processing]]		[[Category: Mrna processing]]

OCA: Protected "3els" [edit=sysop:move=sysop]

OCA — Wed, 09 Jan 2013 09:08:10 GMT

Protected "3els" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:08, 9 January 2013

OCA at 09:08, 9 January 2013

OCA — Wed, 09 Jan 2013 09:08:07 GMT

←Older revision		Revision as of 09:08, 9 January 2013
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-	~~{{Seed}}~~	+	[[Image:3els.png\|left\|200px]]
-	[[Image:3els.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3els", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3els\| PDB=3els \| SCENE= }}		{{STRUCTURE_3els\| PDB=3els \| SCENE= }}

	===Crystal Structure of Yeast Pml1p, Residues 51-204===		===Crystal Structure of Yeast Pml1p, Residues 51-204===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19010333}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19010333 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19010333}}		{{ABSTRACT_PUBMED_19010333}}

	==About this Structure==		==About this Structure==
-	~~3ELS~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ELS OCA].	+	[[3els]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ELS OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19010333~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019010333</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Luehrmann, R.]]		[[Category: Luehrmann, R.]]
Line 29:		Line 17:
	[[Category: Wahl, M C.]]		[[Category: Wahl, M C.]]
	[[Category: Weber, G.]]		[[Category: Weber, G.]]
-	[[Category: Cytoplasm]]
	[[Category: Intrinsically unstructured domain]]		[[Category: Intrinsically unstructured domain]]
	[[Category: Mrna processing]]		[[Category: Mrna processing]]
Line 37:		Line 24:
	[[Category: Protein phosphorylation]]		[[Category: Protein phosphorylation]]
	[[Category: Res complex]]		[[Category: Res complex]]
-	[[Category: ~~X-ray crystallography~~]]	+	[[Category: Splicing]]
-		+
-	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 11 12:42:24 2009''~~	+

OCA at 10:42, 11 February 2009

OCA — Wed, 11 Feb 2009 10:42:25 GMT

←Older revision		Revision as of 10:42, 11 February 2009
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3els.jpg\|left\|200px]]

-	The ~~entry 3els~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3els", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3els\| PDB=3els \| SCENE= }}

-	~~Authors: Trowitzsch~~, ~~S., Weber, G., Luehrmann, R., Wahl, M.C.~~	+	===Crystal Structure of Yeast Pml1p, Residues 51-204===

-	Description: Crystal Structure of Yeast Pml1p, Residues 51-204

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Oct 15 14~~:05:~~51 2008~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19010333}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19010333 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19010333}}
		+
		+	==About this Structure==
		+	3ELS is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ELS OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19010333</ref><references group="xtra"/>
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Luehrmann, R.]]
		+	[[Category: Trowitzsch, S.]]
		+	[[Category: Wahl, M C.]]
		+	[[Category: Weber, G.]]
		+	[[Category: Cytoplasm]]
		+	[[Category: Intrinsically unstructured domain]]
		+	[[Category: Mrna processing]]
		+	[[Category: Mrna splicing]]
		+	[[Category: Nucleus]]
		+	[[Category: Pre-mrna retention and splicing]]
		+	[[Category: Protein phosphorylation]]
		+	[[Category: Res complex]]
		+	[[Category: X-ray crystallography]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 11 12:42:24 2009''

OCA at 12:05, 15 October 2008

OCA — Wed, 15 Oct 2008 12:05:52 GMT

←Older revision		Revision as of 12:05, 15 October 2008
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3els is ON HOLD	+	The entry 3els is ON HOLD until Paper Publication

	Authors: Trowitzsch, S., Weber, G., Luehrmann, R., Wahl, M.C.		Authors: Trowitzsch, S., Weber, G., Luehrmann, R., Wahl, M.C.
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	Description: Crystal Structure of Yeast Pml1p, Residues 51-204		Description: Crystal Structure of Yeast Pml1p, Residues 51-204

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct ~~8 09~~:20:18 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 15 14:05:51 2008''