3hay - Revision history

OCA at 15:48, 1 November 2023

2023-11-01T15:48:10Z

←Older revision		Revision as of 15:48, 1 November 2023
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	<StructureSection load='3hay' size='340' side='right'caption='[[3hay]], [[Resolution\|resolution]] 4.99Å' scene=''>		<StructureSection load='3hay' size='340' side='right'caption='[[3hay]], [[Resolution\|resolution]] 4.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hay]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43587 Atcc 43587~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HAY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hay]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HAY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 4.99Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=FHU:(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5-MONOPHOSPHATE'>FHU</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FHU:(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5-MONOPHOSPHATE'>FHU</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;~~'>~~[[3hax\|3hax]]~~</~~div~~>~~</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB, PF1785 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), PF1791 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), PF1141 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), rpl7ae, PF1367 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</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=3hay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hay OCA], [https://pdbe.org/3hay PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hay RCSB], [https://www.ebi.ac.uk/pdbsum/3hay PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hay 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=3hay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hay OCA], [https://pdbe.org/3hay PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hay RCSB], [https://www.ebi.ac.uk/pdbsum/3hay PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hay ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RL7A_PYRFU RL7A_PYRFU]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity). [[https://www.uniprot.org/uniprot/TRUB_PYRFU TRUB_PYRFU]] Could be responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs ~~(By similarity). [[https://www.uniprot.org/uniprot/NOP10_PYRFU NOP10_PYRFU]] Involved in ribosome biogenesis; more specifically in 18S rRNA pseudouridylation and in cleavage of pre-rRNA~~ (By similarity).	+	[https://www.uniprot.org/uniprot/TRUB_PYRFU TRUB_PYRFU] Could be responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	*[[Pseudouridine synthase 3D structures\|Pseudouridine synthase 3D structures]]		*[[Pseudouridine synthase 3D structures\|Pseudouridine synthase 3D structures]]
	*[[Ribosome biogenesis protein\|Ribosome biogenesis protein]]		*[[Ribosome biogenesis protein\|Ribosome biogenesis protein]]
		+	*[[Ribosome biogenesis protein 3D structures\|Ribosome biogenesis protein 3D structures]]
	*[[User:Wayne Decatur/kink-turn motif\|User:Wayne Decatur/kink-turn motif]]		*[[User:Wayne Decatur/kink-turn motif\|User:Wayne Decatur/kink-turn motif]]
	== References ==		== References ==
Line 42:		Line 41:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43587]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ye, K~~]]	+	[[Category: Pyrococcus furiosus]]
-	[[Category: ~~Guide rna]]~~	+	[[Category: Ye K]]
-	~~[[Category: H/aca]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Isomerase-biosynthetic protein-rna complex]]~~	+
-	~~[[Category: Pseudouridine synthase]]~~	+
-	~~[[Category: Ribonucleoprotein]]~~	+
-	~~[[Category: Ribosomal protein]]~~	+
-	~~[[Category: Ribosome biogenesis]]~~	+
-	~~[[Category: Rna-binding]]~~	+
-	~~[[Category: Rna-protein complex]]~~	+
-	~~[[Category: Rrna processing]]~~	+
-	~~[[Category: Trna processing~~]]	+

OCA at 07:43, 10 November 2021

2021-11-10T07:43:46Z

←Older revision		Revision as of 07:43, 10 November 2021
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	==Crystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus==		==Crystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus==
-	<StructureSection load='3hay' size='340' side='right' caption='[[3hay]], [[Resolution\|resolution]] 4.99Å' scene=''>	+	<StructureSection load='3hay' size='340' side='right'caption='[[3hay]], [[Resolution\|resolution]] 4.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hay]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3HAY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hay]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HAY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FHU:(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5-MONOPHOSPHATE'>FHU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FHU:(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5-MONOPHOSPHATE'>FHU</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hax\|3hax]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3hax\|3hax]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB, PF1785 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), PF1791 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), PF1141 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), rpl7ae, PF1367 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB, PF1785 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), PF1791 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), PF1141 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), rpl7ae, PF1367 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</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=3hay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hay OCA], [~~http~~://pdbe.org/3hay PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3hay RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3hay PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3hay 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=3hay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hay OCA], [https://pdbe.org/3hay PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hay RCSB], [https://www.ebi.ac.uk/pdbsum/3hay PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hay ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RL7A_PYRFU RL7A_PYRFU]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity). [[~~http~~://www.uniprot.org/uniprot/TRUB_PYRFU TRUB_PYRFU]] Could be responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs (By similarity). [[~~http~~://www.uniprot.org/uniprot/NOP10_PYRFU NOP10_PYRFU]] Involved in ribosome biogenesis; more specifically in 18S rRNA pseudouridylation and in cleavage of pre-rRNA (By similarity).	+	[[https://www.uniprot.org/uniprot/RL7A_PYRFU RL7A_PYRFU]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity). [[https://www.uniprot.org/uniprot/TRUB_PYRFU TRUB_PYRFU]] Could be responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs (By similarity). [[https://www.uniprot.org/uniprot/NOP10_PYRFU NOP10_PYRFU]] Involved in ribosome biogenesis; more specifically in 18S rRNA pseudouridylation and in cleavage of pre-rRNA (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	*[[Guide-independent Pseudouridine synthase\|Guide-independent Pseudouridine synthase]]		*[[Guide-independent Pseudouridine synthase\|Guide-independent Pseudouridine synthase]]
	*[[Kink-turn motif\|Kink-turn motif]]		*[[Kink-turn motif\|Kink-turn motif]]
-	*[[~~RNA-guided pseudouridine~~ synthase\|~~RNA-guided pseudouridine~~ synthase]]	+	*[[Pseudouridine synthase 3D structures\|Pseudouridine synthase 3D structures]]
	*[[Ribosome biogenesis protein\|Ribosome biogenesis protein]]		*[[Ribosome biogenesis protein\|Ribosome biogenesis protein]]
	*[[User:Wayne Decatur/kink-turn motif\|User:Wayne Decatur/kink-turn motif]]		*[[User:Wayne Decatur/kink-turn motif\|User:Wayne Decatur/kink-turn motif]]
Line 43:		Line 43:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43587]]		[[Category: Atcc 43587]]
		+	[[Category: Large Structures]]
	[[Category: Ye, K]]		[[Category: Ye, K]]
	[[Category: Guide rna]]		[[Category: Guide rna]]

OCA at 05:40, 7 December 2018

2018-12-07T05:40:13Z

←Older revision		Revision as of 05:40, 7 December 2018
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ha/3hay_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ha/3hay_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>
Line 33:		Line 33:

	==See Also==		==See Also==
		+	*[[Guide-independent Pseudouridine synthase\|Guide-independent Pseudouridine synthase]]
	*[[Kink-turn motif\|Kink-turn motif]]		*[[Kink-turn motif\|Kink-turn motif]]
-	*[[~~TRNA~~ pseudouridine synthase\|~~TRNA~~ pseudouridine synthase]]	+	*[[RNA-guided pseudouridine synthase\|RNA-guided pseudouridine synthase]]
		+	*[[Ribosome biogenesis protein\|Ribosome biogenesis protein]]
	*[[User:Wayne Decatur/kink-turn motif\|User:Wayne Decatur/kink-turn motif]]		*[[User:Wayne Decatur/kink-turn motif\|User:Wayne Decatur/kink-turn motif]]
	== References ==		== References ==

OCA at 17:33, 5 August 2016

2016-08-05T17:33:40Z

←Older revision		Revision as of 17:33, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus==		==Crystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus==
	<StructureSection load='3hay' size='340' side='right' caption='[[3hay]], [[Resolution\|resolution]] 4.99Å' scene=''>		<StructureSection load='3hay' size='340' side='right' caption='[[3hay]], [[Resolution\|resolution]] 4.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hay]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_furiosus Pyrococcus furiosus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HAY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hay]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HAY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FHU:(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5-MONOPHOSPHATE'>FHU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FHU:(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5-MONOPHOSPHATE'>FHU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hax\|3hax]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hax\|3hax]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB, PF1785 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ~~Pyrococcus furiosus~~]), PF1791 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ~~Pyrococcus furiosus~~]), PF1141 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ~~Pyrococcus furiosus~~]), rpl7ae, PF1367 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ~~Pyrococcus furiosus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB, PF1785 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), PF1791 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), PF1141 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), rpl7ae, PF1367 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</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=3hay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hay OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hay RCSB], [http://www.ebi.ac.uk/pdbsum/3hay 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=3hay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hay OCA], [http://pdbe.org/3hay PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hay RCSB], [http://www.ebi.ac.uk/pdbsum/3hay PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hay ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=3hay ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 3hay" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 40:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrococcus furiosus~~]]	+	[[Category: Atcc 43587]]
	[[Category: Ye, K]]		[[Category: Ye, K]]
	[[Category: Guide rna]]		[[Category: Guide rna]]

OCA at 20:40, 25 December 2014

2014-12-25T20:40:21Z

←Older revision		Revision as of 20:40, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3hay\| PDB=3hay \| SCENE= }}~~	+	==Crystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus==
-	===Crystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus===	+	<StructureSection load='3hay' size='340' side='right' caption='[[3hay]], [[Resolution\|resolution]] 4.99Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19481523}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3hay]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HAY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FHU:(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5-MONOPHOSPHATE'>FHU</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hax\|3hax]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB, PF1785 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus]), PF1791 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus]), PF1141 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus]), rpl7ae, PF1367 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus])</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=3hay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hay OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hay RCSB], [http://www.ebi.ac.uk/pdbsum/3hay PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RL7A_PYRFU RL7A_PYRFU]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity). [[http://www.uniprot.org/uniprot/TRUB_PYRFU TRUB_PYRFU]] Could be responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs (By similarity). [[http://www.uniprot.org/uniprot/NOP10_PYRFU NOP10_PYRFU]] Involved in ribosome biogenesis; more specifically in 18S rRNA pseudouridylation and in cleavage of pre-rRNA (By similarity).
		+	== 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/ha/3hay_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 ==
		+	H/ACA RNAs form ribonucleoprotein complex (RNP) with proteins Cbf5, Nop10, L7Ae, and Gar1 and guide site-specific conversion of uridine into pseudouridine in cellular RNAs. The crystal structures of H/ACA RNP with substrate bound at the active site cleft reveal that the substrate is recruited through sequence-specific pairing with guide RNA and essential protein contacts. Substrate binding leads to a reorganization of a preset pseudouridylation pocket and an adaptive movement of the PUA domain and the lower stem of the H/ACA RNA. Moreover, a thumb loop flips from the Gar1-bound state in the substrate-free RNP structure to tightly associate with the substrate. Mutagenesis and enzyme kinetics analysis suggest a critical role of Gar1 and the thumb in substrate turnover, particularly in product release. Comparison with tRNA Psi55 synthase TruB reveals the structural conservation and adaptation between an RNA-guided and stand-alone pseudouridine synthase and provides insight into the guide-independent activity of Cbf5.

-	~~==About this Structure==~~	+	Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase.,Duan J, Li L, Lu J, Wang W, Ye K Mol Cell. 2009 May 14;34(4):427-39. PMID:19481523<ref>PMID:19481523</ref>
-	~~[[3hay]] is a 6 chain structure with sequence from [http:~~/~~/en~~.~~wikipedia~~.~~org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3HAY OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Kink-turn motif\|Kink-turn motif]]		*[[Kink-turn motif\|Kink-turn motif]]
-	*[[~~Ribosomal protein L7~~\|~~Ribosomal protein L7~~]]	+	*[[TRNA pseudouridine synthase\|TRNA pseudouridine synthase]]
	*[[User:Wayne Decatur/kink-turn motif\|User:Wayne Decatur/kink-turn motif]]		*[[User:Wayne Decatur/kink-turn motif\|User:Wayne Decatur/kink-turn motif]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019481523<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Pyrococcus furiosus]]		[[Category: Pyrococcus furiosus]]
-	[[Category: Ye, K.]]	+	[[Category: Ye, K]]
	[[Category: Guide rna]]		[[Category: Guide rna]]
	[[Category: H/aca]]		[[Category: H/aca]]

OCA at 11:01, 11 March 2013

2013-03-11T11:01:20Z

←Older revision		Revision as of 11:01, 11 March 2013
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-	[[Image:3hay.png\|left\|200px]]
-
	{{STRUCTURE_3hay\| PDB=3hay \| SCENE= }}		{{STRUCTURE_3hay\| PDB=3hay \| SCENE= }}
-
	===Crystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus===		===Crystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus===
-
	{{ABSTRACT_PUBMED_19481523}}		{{ABSTRACT_PUBMED_19481523}}

OCA at 21:22, 20 October 2012

2012-10-20T21:22:03Z

←Older revision		Revision as of 21:22, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3hay]] is a 6 chain structure ~~of [[Kink-turn motif]], [[Ribosomal protein L7]] and [[User:Wayne Decatur/kink-turn motif]]~~ with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAY OCA].	+	[[3hay]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAY OCA].

	==See Also==		==See Also==

OCA at 13:02, 27 July 2012

2012-07-27T13:02:33Z

←Older revision		Revision as of 13:02, 27 July 2012
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	[[Image:3hay.png\|left\|200px]]		[[Image:3hay.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_3hay\| PDB=3hay \| SCENE= }}		{{STRUCTURE_3hay\| PDB=3hay \| SCENE= }}

	===Crystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus===		===Crystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus===

-
-	<!--
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	{{ABSTRACT_PUBMED_19481523}}		{{ABSTRACT_PUBMED_19481523}}

	==About this Structure==		==About this Structure==
-	[[3hay]] is a 6 chain structure of [[Ribosomal protein L7]] with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAY OCA].	+	[[3hay]] is a 6 chain structure of [[Kink-turn motif]], [[Ribosomal protein L7]] and [[User:Wayne Decatur/kink-turn motif]] with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAY OCA].

	==See Also==		==See Also==
-	*[[Ribosomal protein L7]]	+	*[[Kink-turn motif\|Kink-turn motif]]
		+	*[[Ribosomal protein L7\|Ribosomal protein L7]]
		+	*[[User:Wayne Decatur/kink-turn motif\|User:Wayne Decatur/kink-turn motif]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19481523~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019481523</ref><references group="xtra"/>
	[[Category: Pyrococcus furiosus]]		[[Category: Pyrococcus furiosus]]
	[[Category: Ye, K.]]		[[Category: Ye, K.]]
Line 31:		Line 22:
	[[Category: H/aca]]		[[Category: H/aca]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
-	[[Category: Isomerase/biosynthetic protein/rna complex]]	+	[[Category: Isomerase-biosynthetic protein-rna complex]]
	[[Category: Pseudouridine synthase]]		[[Category: Pseudouridine synthase]]
	[[Category: Ribonucleoprotein]]		[[Category: Ribonucleoprotein]]

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

2010-12-26T22:56:44Z

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

←Older revision

Revision as of 22:56, 26 December 2010

OCA at 22:56, 26 December 2010

2010-12-26T22:56:43Z

←Older revision		Revision as of 22:56, 26 December 2010
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-	~~{{Seed}}~~	+	[[Image:3hay.png\|left\|200px]]
-	[[Image:3hay.~~jpg~~\|left\|200px]]	+

	<!--		<!--
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	==About this Structure==		==About this Structure==
-	~~3HAY~~ is a 6 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAY OCA].	+	[[3hay]] is a 6 chain structure of [[Ribosomal protein L7]] with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAY OCA].
		+
		+	==See Also==
		+	*[[Ribosomal protein L7]]

	==Reference==		==Reference==
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	[[Category: Rrna processing]]		[[Category: Rrna processing]]
	[[Category: Trna processing]]		[[Category: Trna processing]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 25 09:04:42 2009''