1sj4 - Revision history

OCA at 08:31, 14 February 2024

OCA — Wed, 14 Feb 2024 08:31:08 GMT

←Older revision		Revision as of 08:31, 14 February 2024
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	<StructureSection load='1sj4' size='340' side='right'caption='[[1sj4]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1sj4' size='340' side='right'caption='[[1sj4]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sj4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ ] and [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SJ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sj4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Hepatitis_delta_virus Hepatitis delta virus] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SJ4 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1cx0\|1cx0]], [[1drz\|1drz]], [[1sj3\|1sj3]]</div></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]] 2.7Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">SNRPA ([https://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'>[https://proteopedia.org/fgij/fg.htm?mol=1sj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sj4 OCA], [https://pdbe.org/1sj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sj4 RCSB], [https://www.ebi.ac.uk/pdbsum/1sj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sj4 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=1sj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sj4 OCA], [https://pdbe.org/1sj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sj4 RCSB], [https://www.ebi.ac.uk/pdbsum/1sj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sj4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>	+	[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1sj4 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=1sj4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2'-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical similarity to protein ribonucleases and to zymogens for which conformational dynamics are integral to biological activity. This finding implies that RNA structural rearrangements control the reactivity of ribozymes and ribonucleoprotein enzymes.
-
-	A conformational switch controls hepatitis delta virus ribozyme catalysis.,Ke A, Zhou K, Ding F, Cate JH, Doudna JA Nature. 2004 May 13;429(6988):201-5. PMID:15141216<ref>PMID:15141216</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1sj4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]		*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]
-	*[[Ribozyme\|Ribozyme]]	+	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Hepatitis delta virus]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cate~~, J H~~]]	+	[[Category: Cate JH]]
-	[[Category: Ding, F]]	+	[[Category: Ding F]]
-	[[Category: Doudna~~, J A~~]]	+	[[Category: Doudna JA]]
-	[[Category: Ke, A]]	+	[[Category: Ke A]]
-	[[Category: Zhou, K]]	+	[[Category: Zhou K]]
-	~~[[Category: Hdv]]~~	+
-	~~[[Category: Precurosr]]~~	+
-	~~[[Category: Ribozyme]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Translation-rna complex]]~~	+
-	~~[[Category: U1a~~]]	+

OCA at 15:33, 27 October 2021

OCA — Wed, 27 Oct 2021 15:33:18 GMT

←Older revision		Revision as of 15:33, 27 October 2021
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	<StructureSection load='1sj4' size='340' side='right'caption='[[1sj4]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1sj4' size='340' side='right'caption='[[1sj4]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sj4]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/ ] and [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1SJ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sj4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ ] and [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SJ4 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1cx0\|1cx0]], [[1drz\|1drz]], [[1sj3\|1sj3]]</div></td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1cx0\|1cx0]], [[1drz\|1drz]], [[1sj3\|1sj3]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([https://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~~://proteopedia.org/fgij/fg.htm?mol=1sj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sj4 OCA], [~~http~~://pdbe.org/1sj4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1sj4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1sj4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1sj4 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=1sj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sj4 OCA], [https://pdbe.org/1sj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sj4 RCSB], [https://www.ebi.ac.uk/pdbsum/1sj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sj4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>	+	[[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 11:27, 24 December 2020

OCA — Thu, 24 Dec 2020 11:27:06 GMT

←Older revision		Revision as of 11:27, 24 December 2020
Line 1:		Line 1:

	==Crystal structure of a C75U mutant Hepatitis Delta Virus ribozyme precursor, in Cu2+ solution==		==Crystal structure of a C75U mutant Hepatitis Delta Virus ribozyme precursor, in Cu2+ solution==
-	<StructureSection load='1sj4' size='340' side='right' caption='[[1sj4]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='1sj4' size='340' side='right'caption='[[1sj4]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sj4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SJ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sj4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1SJ4 FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cx0\|1cx0]], [[1drz\|1drz]], [[1sj3\|1sj3]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1cx0\|1cx0]], [[1drz\|1drz]], [[1sj3\|1sj3]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([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=1sj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sj4 OCA], [http://pdbe.org/1sj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sj4 RCSB], [http://www.ebi.ac.uk/pdbsum/1sj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sj4 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1sj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sj4 OCA], [http://pdbe.org/1sj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sj4 RCSB], [http://www.ebi.ac.uk/pdbsum/1sj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sj4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Nucleoprotein\|Nucleoprotein]]	+	*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]
	*[[Ribozyme\|Ribozyme]]		*[[Ribozyme\|Ribozyme]]
	== References ==		== References ==
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Cate, J H]]		[[Category: Cate, J H]]
	[[Category: Ding, F]]		[[Category: Ding, F]]

OCA at 08:03, 14 March 2018

OCA — Wed, 14 Mar 2018 08:03:21 GMT

←Older revision		Revision as of 08:03, 14 March 2018
Line 1:		Line 1:
		+
	==Crystal structure of a C75U mutant Hepatitis Delta Virus ribozyme precursor, in Cu2+ solution==		==Crystal structure of a C75U mutant Hepatitis Delta Virus ribozyme precursor, in Cu2+ solution==
	<StructureSection load='1sj4' size='340' side='right' caption='[[1sj4]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1sj4' size='340' side='right' caption='[[1sj4]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cx0\|1cx0]], [[1drz\|1drz]], [[1sj3\|1sj3]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cx0\|1cx0]], [[1drz\|1drz]], [[1sj3\|1sj3]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([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=1sj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sj4 OCA], [http://pdbe.org/1sj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sj4 RCSB], [http://www.ebi.ac.uk/pdbsum/1sj4 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=1sj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sj4 OCA], [http://pdbe.org/1sj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sj4 RCSB], [http://www.ebi.ac.uk/pdbsum/1sj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sj4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sj/1sj4_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sj/1sj4_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 11:51, 7 February 2016

OCA — Sun, 07 Feb 2016 11:51:00 GMT

←Older revision		Revision as of 11:51, 7 February 2016
Line 17:		Line 17:
	<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=1sj4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:13, 10 September 2015

OCA — Thu, 10 Sep 2015 01:13:46 GMT

←Older revision		Revision as of 01:13, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1sj4' size='340' side='right' caption='[[1sj4]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1sj4' size='340' side='right' caption='[[1sj4]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sj4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Hepatitis_delta_virus Hepatitis delta virus~~] and [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SJ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sj4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SJ4 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cx0\|1cx0]], [[1drz\|1drz]], [[1sj3\|1sj3]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cx0\|1cx0]], [[1drz\|1drz]], [[1sj3\|1sj3]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([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=1sj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sj4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sj4 RCSB], [http://www.ebi.ac.uk/pdbsum/1sj4 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=1sj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sj4 OCA], [http://pdbe.org/1sj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sj4 RCSB], [http://www.ebi.ac.uk/pdbsum/1sj4 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1sj4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hepatitis delta virus]]~~	+	[[Category: Human]]
-	~~[[Category: Homo sapiens~~]]	+
	[[Category: Cate, J H]]		[[Category: Cate, J H]]
	[[Category: Ding, F]]		[[Category: Ding, F]]

OCA at 14:52, 24 December 2014

OCA — Wed, 24 Dec 2014 14:52:20 GMT

←Older revision		Revision as of 14:52, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1sj4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Hepatitis_delta_virus Hepatitis delta virus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SJ4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1sj4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Hepatitis_delta_virus Hepatitis delta virus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SJ4 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cx0\|1cx0]], [[1drz\|1drz]], [[1sj3\|1sj3]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cx0\|1cx0]], [[1drz\|1drz]], [[1sj3\|1sj3]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sj4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sj4 RCSB], [http://www.ebi.ac.uk/pdbsum/1sj4 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=1sj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sj4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sj4 RCSB], [http://www.ebi.ac.uk/pdbsum/1sj4 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Hepatitis delta virus]]		[[Category: Hepatitis delta virus]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Cate, J H.]]	+	[[Category: Cate, J H]]
-	[[Category: Ding, F.]]	+	[[Category: Ding, F]]
-	[[Category: Doudna, J A.]]	+	[[Category: Doudna, J A]]
-	[[Category: Ke, A.]]	+	[[Category: Ke, A]]
-	[[Category: Zhou, K.]]	+	[[Category: Zhou, K]]
	[[Category: Hdv]]		[[Category: Hdv]]
	[[Category: Precurosr]]		[[Category: Precurosr]]

OCA at 22:35, 28 September 2014

OCA — Sun, 28 Sep 2014 22:35:50 GMT

←Older revision		Revision as of 22:35, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1sj4.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of a C75U mutant Hepatitis Delta Virus ribozyme precursor, in Cu2+ solution==
		+	<StructureSection load='1sj4' size='340' side='right' caption='[[1sj4]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1sj4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Hepatitis_delta_virus Hepatitis delta virus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SJ4 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cx0\|1cx0]], [[1drz\|1drz]], [[1sj3\|1sj3]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sj4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sj4 RCSB], [http://www.ebi.ac.uk/pdbsum/1sj4 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/sj/1sj4_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 ==
		+	Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2'-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical similarity to protein ribonucleases and to zymogens for which conformational dynamics are integral to biological activity. This finding implies that RNA structural rearrangements control the reactivity of ribozymes and ribonucleoprotein enzymes.

-	~~{{STRUCTURE_1sj4\| PDB=1sj4 \| SCENE= }}~~	+	A conformational switch controls hepatitis delta virus ribozyme catalysis.,Ke A, Zhou K, Ding F, Cate JH, Doudna JA Nature. 2004 May 13;429(6988):201-5. PMID:15141216<ref>PMID:15141216</ref>

-	~~===Crystal structure of a C75U mutant Hepatitis Delta Virus ribozyme precursor~~, ~~in Cu2+ solution===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15141216}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1sj4]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Hepatitis_delta_virus Hepatitis delta virus] and [http://en~~.~~wikipedia.org~~/~~wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA].~~	+

	==See Also==		==See Also==
	*[[Nucleoprotein\|Nucleoprotein]]		*[[Nucleoprotein\|Nucleoprotein]]
	*[[Ribozyme\|Ribozyme]]		*[[Ribozyme\|Ribozyme]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015141216<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Hepatitis delta virus]]		[[Category: Hepatitis delta virus]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA at 06:33, 20 October 2012

OCA — Sat, 20 Oct 2012 06:33:08 GMT

←Older revision		Revision as of 06:33, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1sj4]] is a 2 chain structure ~~of [[Nucleoprotein]] and [[Ribozyme]]~~ with sequence from [http://en.wikipedia.org/wiki/Hepatitis_delta_virus Hepatitis delta virus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA].	+	[[1sj4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Hepatitis_delta_virus Hepatitis delta virus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA].

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

OCA at 13:32, 25 July 2012

OCA — Wed, 25 Jul 2012 13:32:50 GMT

←Older revision		Revision as of 13:32, 25 July 2012
Line 1:		Line 1:
	[[Image:1sj4.png\|left\|200px]]		[[Image:1sj4.png\|left\|200px]]

-	<!--
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-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
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	{{STRUCTURE_1sj4\| PDB=1sj4 \| SCENE= }}		{{STRUCTURE_1sj4\| PDB=1sj4 \| SCENE= }}

	===Crystal structure of a C75U mutant Hepatitis Delta Virus ribozyme precursor, in Cu2+ solution===		===Crystal structure of a C75U mutant Hepatitis Delta Virus ribozyme precursor, in Cu2+ solution===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15141216}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15141216 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_15141216}}		{{ABSTRACT_PUBMED_15141216}}

	==About this Structure==		==About this Structure==
-	[[1sj4]] is a 2 chain structure of [[Ribozyme]] with sequence from [http://en.wikipedia.org/wiki/Hepatitis_delta_virus Hepatitis delta virus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA].	+	[[1sj4]] is a 2 chain structure of [[Nucleoprotein]] and [[Ribozyme]] with sequence from [http://en.wikipedia.org/wiki/Hepatitis_delta_virus Hepatitis delta virus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJ4 OCA].

	==See Also==		==See Also==
-	*[[Ribozyme]]	+	*[[Nucleoprotein\|Nucleoprotein]]
		+	*[[Ribozyme\|Ribozyme]]

	==Reference==		==Reference==