2r8f - Revision history

OCA at 09:03, 25 October 2023

OCA — Wed, 25 Oct 2023 09:03:25 GMT

←Older revision		Revision as of 09:03, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='2r8f' size='340' side='right'caption='[[2r8f]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2r8f' size='340' side='right'caption='[[2r8f]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r8f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Rotsr Rotsr~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R8F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r8f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Simian_11_rotavirus_(serotype_3_/_strain_SA11-Ramig) Simian 11 rotavirus (serotype 3 / strain SA11-Ramig)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R8F FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID~~-~~ADENYLATE+ESTER'>AGS</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1l9v\|1l9v]], [[2r7c\|2r7c]], [[2r7j\|2r7j]], [[2r7p\|2r7p]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">S8, SEGMENT 8 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36435 ROTSR])~~</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=2r8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8f OCA], [https://pdbe.org/2r8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r8f RCSB], [https://www.ebi.ac.uk/pdbsum/2r8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8f 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=2r8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8f OCA], [https://pdbe.org/2r8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r8f RCSB], [https://www.ebi.ac.uk/pdbsum/2r8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NSP2_ROTSR NSP2_ROTSR]] Involved in genome replication and packaging. Plays a crucial role, together with NSP5, in the formation of virus factories (viroplasms) which are large inclusions in the cytoplasm where replication intermediates are assembled and RNA replication takes place. Displays ssRNA binding, NTPase, RNA triphosphatase (RTPase) and ATP-independent helix-unwinding activity activities. The unwiding activity may prepare and organize plus-strand RNAs for packaging and replication by removing interfering secondary structures. Unlike typical helicases, NSP2 requires neither a divalent cation nor a nucleotide energy source for helix destabilization. The RTPase activity may account for the absence of the 5'-terminal gamma-phosphate on the minus-strands of dsRNA genome segments (By similarity).	+	[https://www.uniprot.org/uniprot/NSP2_ROTSR NSP2_ROTSR] Involved in genome replication and packaging. Plays a crucial role, together with NSP5, in the formation of virus factories (viroplasms) which are large inclusions in the cytoplasm where replication intermediates are assembled and RNA replication takes place. Displays ssRNA binding, NTPase, RNA triphosphatase (RTPase) and ATP-independent helix-unwinding activity activities. The unwiding activity may prepare and organize plus-strand RNAs for packaging and replication by removing interfering secondary structures. Unlike typical helicases, NSP2 requires neither a divalent cation nor a nucleotide energy source for helix destabilization. The RTPase activity may account for the absence of the 5'-terminal gamma-phosphate on the minus-strands of dsRNA genome segments (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Rotsr]]~~	+	[[Category: Kumar M]]
-	[[Category: Kumar, M]]	+	[[Category: Prasad BVV]]
-	[[Category: Prasad~~, B V.V]]~~	+
-	~~[[Category: Ndp kinase]]~~	+
-	~~[[Category: Non structural protein]]~~	+
-	~~[[Category: Ntpase]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Rna-binding]]~~	+
-	~~[[Category: Rotavirus~~]]	+

OCA at 04:17, 2 July 2021

OCA — Fri, 02 Jul 2021 04:17:56 GMT

←Older revision		Revision as of 04:17, 2 July 2021
Line 1:		Line 1:

	==Crystal structure of H225A NSP2 and ATP-gS complex==		==Crystal structure of H225A NSP2 and ATP-gS complex==
-	<StructureSection load='2r8f' size='340' side='right' caption='[[2r8f]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='2r8f' size='340' side='right'caption='[[2r8f]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r8f]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Rotsr Rotsr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2R8F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r8f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rotsr Rotsr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R8F FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l9v\|1l9v]], [[2r7c\|2r7c]], [[2r7j\|2r7j]], [[2r7p\|2r7p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1l9v\|1l9v]], [[2r7c\|2r7c]], [[2r7j\|2r7j]], [[2r7p\|2r7p]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S8, SEGMENT 8 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36435 ROTSR])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S8, SEGMENT 8 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36435 ROTSR])</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=2r8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8f OCA], [~~http~~://pdbe.org/2r8f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2r8f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2r8f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8f 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=2r8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8f OCA], [https://pdbe.org/2r8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r8f RCSB], [https://www.ebi.ac.uk/pdbsum/2r8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NSP2_ROTSR NSP2_ROTSR]] Involved in genome replication and packaging. Plays a crucial role, together with NSP5, in the formation of virus factories (viroplasms) which are large inclusions in the cytoplasm where replication intermediates are assembled and RNA replication takes place. Displays ssRNA binding, NTPase, RNA triphosphatase (RTPase) and ATP-independent helix-unwinding activity activities. The unwiding activity may prepare and organize plus-strand RNAs for packaging and replication by removing interfering secondary structures. Unlike typical helicases, NSP2 requires neither a divalent cation nor a nucleotide energy source for helix destabilization. The RTPase activity may account for the absence of the 5'-terminal gamma-phosphate on the minus-strands of dsRNA genome segments (By similarity).	+	[[https://www.uniprot.org/uniprot/NSP2_ROTSR NSP2_ROTSR]] Involved in genome replication and packaging. Plays a crucial role, together with NSP5, in the formation of virus factories (viroplasms) which are large inclusions in the cytoplasm where replication intermediates are assembled and RNA replication takes place. Displays ssRNA binding, NTPase, RNA triphosphatase (RTPase) and ATP-independent helix-unwinding activity activities. The unwiding activity may prepare and organize plus-strand RNAs for packaging and replication by removing interfering secondary structures. Unlike typical helicases, NSP2 requires neither a divalent cation nor a nucleotide energy source for helix destabilization. The RTPase activity may account for the absence of the 5'-terminal gamma-phosphate on the minus-strands of dsRNA genome segments (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Rotsr]]		[[Category: Rotsr]]
	[[Category: Kumar, M]]		[[Category: Kumar, M]]

OCA at 10:47, 5 September 2018

OCA — Wed, 05 Sep 2018 10:47:51 GMT

←Older revision		Revision as of 10:47, 5 September 2018
Line 1:		Line 1:
		+
	==Crystal structure of H225A NSP2 and ATP-gS complex==		==Crystal structure of H225A NSP2 and ATP-gS complex==
	<StructureSection load='2r8f' size='340' side='right' caption='[[2r8f]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2r8f' size='340' side='right' caption='[[2r8f]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l9v\|1l9v]], [[2r7c\|2r7c]], [[2r7j\|2r7j]], [[2r7p\|2r7p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l9v\|1l9v]], [[2r7c\|2r7c]], [[2r7j\|2r7j]], [[2r7p\|2r7p]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S8, SEGMENT 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36435 ROTSR])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S8, SEGMENT 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36435 ROTSR])</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=2r8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8f OCA], [http://pdbe.org/2r8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r8f RCSB], [http://www.ebi.ac.uk/pdbsum/2r8f 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=2r8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8f OCA], [http://pdbe.org/2r8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r8f RCSB], [http://www.ebi.ac.uk/pdbsum/2r8f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8f 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/r8/2r8f_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r8/2r8f_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 02:09, 9 February 2016

OCA — Tue, 09 Feb 2016 02:09:45 GMT

←Older revision		Revision as of 02:09, 9 February 2016
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=2r8f ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:35, 10 September 2015

OCA — Thu, 10 Sep 2015 17:35:16 GMT

←Older revision		Revision as of 17:35, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2r8f' size='340' side='right' caption='[[2r8f]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2r8f' size='340' side='right' caption='[[2r8f]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r8f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Viruses Viruses~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r8f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rotsr Rotsr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l9v\|1l9v]], [[2r7c\|2r7c]], [[2r7j\|2r7j]], [[2r7p\|2r7p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l9v\|1l9v]], [[2r7c\|2r7c]], [[2r7j\|2r7j]], [[2r7p\|2r7p]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S8, SEGMENT 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~10239 Viruses~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S8, SEGMENT 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36435 ROTSR])</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=2r8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r8f RCSB], [http://www.ebi.ac.uk/pdbsum/2r8f 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=2r8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8f OCA], [http://pdbe.org/2r8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r8f RCSB], [http://www.ebi.ac.uk/pdbsum/2r8f PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~VN35_ROTSR VN35_ROTSR~~]] Involved in genome replication and packaging. Plays a crucial role, together with NSP5, in the formation of virus factories (viroplasms) which are large inclusions in the cytoplasm where replication intermediates are assembled and RNA replication takes place. Displays ssRNA binding, NTPase, RNA triphosphatase (RTPase) and ATP-independent helix-unwinding activity activities. The unwiding activity may prepare and organize plus-strand RNAs for packaging and replication by removing interfering secondary structures. Unlike typical helicases, NSP2 requires neither a divalent cation nor a nucleotide energy source for helix destabilization. The RTPase activity may account for the absence of the 5'-terminal gamma-phosphate on the minus-strands of dsRNA genome segments (By similarity).	+	[[http://www.uniprot.org/uniprot/NSP2_ROTSR NSP2_ROTSR]] Involved in genome replication and packaging. Plays a crucial role, together with NSP5, in the formation of virus factories (viroplasms) which are large inclusions in the cytoplasm where replication intermediates are assembled and RNA replication takes place. Displays ssRNA binding, NTPase, RNA triphosphatase (RTPase) and ATP-independent helix-unwinding activity activities. The unwiding activity may prepare and organize plus-strand RNAs for packaging and replication by removing interfering secondary structures. Unlike typical helicases, NSP2 requires neither a divalent cation nor a nucleotide energy source for helix destabilization. The RTPase activity may account for the absence of the 5'-terminal gamma-phosphate on the minus-strands of dsRNA genome segments (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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 2r8f" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Viruses~~]]	+	[[Category: Rotsr]]
	[[Category: Kumar, M]]		[[Category: Kumar, M]]
	[[Category: Prasad, B V.V]]		[[Category: Prasad, B V.V]]

OCA at 03:41, 25 December 2014

OCA — Thu, 25 Dec 2014 03:41:44 GMT

←Older revision		Revision as of 03:41, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2r8f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8F FirstGlance]. <br>		<table><tr><td colspan='2'>[[2r8f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8F FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l9v\|1l9v]], [[2r7c\|2r7c]], [[2r7j\|2r7j]], [[2r7p\|2r7p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l9v\|1l9v]], [[2r7c\|2r7c]], [[2r7j\|2r7j]], [[2r7p\|2r7p]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S8, SEGMENT 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10239 Viruses])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S8, SEGMENT 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10239 Viruses])</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=2r8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r8f RCSB], [http://www.ebi.ac.uk/pdbsum/2r8f 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=2r8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r8f RCSB], [http://www.ebi.ac.uk/pdbsum/2r8f PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VN35_ROTSR VN35_ROTSR]] Involved in genome replication and packaging. Plays a crucial role, together with NSP5, in the formation of virus factories (viroplasms) which are large inclusions in the cytoplasm where replication intermediates are assembled and RNA replication takes place. Displays ssRNA binding, NTPase, RNA triphosphatase (RTPase) and ATP-independent helix-unwinding activity activities. The unwiding activity may prepare and organize plus-strand RNAs for packaging and replication by removing interfering secondary structures. Unlike typical helicases, NSP2 requires neither a divalent cation nor a nucleotide energy source for helix destabilization. The RTPase activity may account for the absence of the 5'-terminal gamma-phosphate on the minus-strands of dsRNA genome segments (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Viruses]]		[[Category: Viruses]]
-	[[Category: Kumar, M.]]	+	[[Category: Kumar, M]]
-	[[Category: Prasad, B V.V.]]	+	[[Category: Prasad, B V.V]]
	[[Category: Ndp kinase]]		[[Category: Ndp kinase]]
	[[Category: Non structural protein]]		[[Category: Non structural protein]]

OCA at 19:12, 30 September 2014

OCA — Tue, 30 Sep 2014 19:12:05 GMT

←Older revision		Revision as of 19:12, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2r8f.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of H225A NSP2 and ATP-gS complex==
		+	<StructureSection load='2r8f' size='340' side='right' caption='[[2r8f]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2r8f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8F FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1l9v\|1l9v]], [[2r7c\|2r7c]], [[2r7j\|2r7j]], [[2r7p\|2r7p]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S8, SEGMENT 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10239 Viruses])</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=2r8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r8f RCSB], [http://www.ebi.ac.uk/pdbsum/2r8f 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/r8/2r8f_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 ==
		+	Rotavirus, the major pathogen of infantile gastroenteritis, carries a nonstructural protein, NSP2, essential for viroplasm formation and genome replication/packaging. In addition to RNA-binding and helix-destabilizing properties, NSP2 exhibits nucleoside triphosphatase activity. A conserved histidine (H225) functions as the catalytic residue for this enzymatic activity, and mutation of this residue abrogates genomic double-stranded RNA synthesis without affecting viroplasm formation. To understand the structural basis of the phosphatase activity of NSP2, we performed crystallographic analyses of native NSP2 and a functionally defective H225A mutant in the presence of nucleotides. These studies showed that nucleotides bind inside a cleft between the two domains of NSP2 in a region that exhibits structural similarity to ubiquitous cellular HIT (histidine triad) proteins. Only minor conformational alterations were observed in the cleft upon nucleotide binding and hydrolysis. This hydrolysis involved the formation of a stable phosphohistidine intermediate. These observations, reminiscent of cellular nucleoside diphosphate (NDP) kinases, prompted us to investigate whether NSP2 exhibits phosphoryl-transfer activity. Bioluminometric assay showed that NSP2 exhibits an NDP kinase-like activity that transfers the bound phosphate to NDPs. However, NSP2 is distinct from the highly conserved cellular NDP kinases in both its structure and catalytic mechanism, thus making NSP2 a potential target for antiviral drug design. With structural similarities to HIT proteins, which are not known to exhibit NDP kinase activity, NSP2 represents a unique example among structure-activity relationships. The newly observed phosphoryl-transfer activity of NSP2 may be utilized for homeostasis of nucleotide pools in viroplasms during genome replication.

-	~~{{STRUCTURE_2r8f\| PDB=2r8f \| SCENE= }}~~	+	Crystallographic and biochemical analysis of rotavirus NSP2 with nucleotides reveals a nucleoside diphosphate kinase-like activity.,Kumar M, Jayaram H, Vasquez-Del Carpio R, Jiang X, Taraporewala ZF, Jacobson RH, Patton JT, Prasad BV J Virol. 2007 Nov;81(22):12272-84. Epub 2007 Sep 5. PMID:17804496<ref>PMID:17804496</ref>

-	~~===Crystal structure~~ of ~~H225A NSP2 and ATP-gS complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17804496}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2r8f]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Viruses Viruses]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2R8F OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017804496<~~/~~ref~~><~~ref group="xtra">PMID:012015608</ref><references group="xtra"~~/>	+
	[[Category: Viruses]]		[[Category: Viruses]]
	[[Category: Kumar, M.]]		[[Category: Kumar, M.]]

OCA at 12:57, 30 January 2013

OCA — Wed, 30 Jan 2013 12:57:47 GMT

←Older revision		Revision as of 12:57, 30 January 2013
Line 1:		Line 1:
	[[Image:2r8f.png\|left\|200px]]		[[Image:2r8f.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2r8f", 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_2r8f\| PDB=2r8f \| SCENE= }}		{{STRUCTURE_2r8f\| PDB=2r8f \| SCENE= }}

	===Crystal structure of H225A NSP2 and ATP-gS complex===		===Crystal structure of H225A NSP2 and ATP-gS complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17804496}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17804496 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17804496}}		{{ABSTRACT_PUBMED_17804496}}

Line 22:		Line 11:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17804496~~</ref><ref group="xtra">PMID:~~12015608~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017804496</ref><ref group="xtra">PMID:012015608</ref><references group="xtra"/>
	[[Category: Viruses]]		[[Category: Viruses]]
	[[Category: Kumar, M.]]		[[Category: Kumar, M.]]

OCA: Protected "2r8f" [edit=sysop:move=sysop]

OCA — Mon, 14 Mar 2011 21:24:22 GMT

Protected "2r8f" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:24, 14 March 2011

OCA at 21:24, 14 March 2011

OCA — Mon, 14 Mar 2011 21:24:20 GMT

←Older revision		Revision as of 21:24, 14 March 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2r8f.png\|left\|200px]]		[[Image:2r8f.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~2R8F~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/~~Simian_rotavirus_a/sa11 Simian rotavirus a/sa11~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8F OCA].	+	[[2r8f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8F OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:17804496</ref><ref group="xtra">PMID:12015608</ref><references group="xtra"/>		<ref group="xtra">PMID:17804496</ref><ref group="xtra">PMID:12015608</ref><references group="xtra"/>
-	[[Category: ~~Simian rotavirus a/sa11~~]]	+	[[Category: Viruses]]
	[[Category: Kumar, M.]]		[[Category: Kumar, M.]]
	[[Category: Prasad, B V.V.]]		[[Category: Prasad, B V.V.]]
Line 33:		Line 32:
	[[Category: Rna-binding]]		[[Category: Rna-binding]]
	[[Category: Rotavirus]]		[[Category: Rotavirus]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:36:53 2009''