2rb4 - Revision history

OCA at 11:52, 30 August 2023

OCA — Wed, 30 Aug 2023 11:52:47 GMT

←Older revision		Revision as of 11:52, 30 August 2023
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	<StructureSection load='2rb4' size='340' side='right'caption='[[2rb4]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2rb4' size='340' side='right'caption='[[2rb4]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rb4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RB4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rb4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RB4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.8Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDX25, GRTH ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2rb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb4 OCA], [https://pdbe.org/2rb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rb4 RCSB], [https://www.ebi.ac.uk/pdbsum/2rb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rb4 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=2rb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb4 OCA], [https://pdbe.org/2rb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rb4 RCSB], [https://www.ebi.ac.uk/pdbsum/2rb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rb4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DDX25_HUMAN DDX25_HUMAN]] ATP-dependent RNA helicase. Required for mRNA export and translation regulation during spermatid development (By similarity).<ref>PMID:10608860</ref>	+	[https://www.uniprot.org/uniprot/DDX25_HUMAN DDX25_HUMAN] ATP-dependent RNA helicase. Required for mRNA export and translation regulation during spermatid development (By similarity).<ref>PMID:10608860</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arrowsmith~~, C H]]~~	+	[[Category: Arrowsmith CH]]
-	~~[[Category: Berg, S Van den~~]]	+	[[Category: Berglund H]]
-	[[Category: Berglund, H]]	+	[[Category: Edwards AM]]
-	[[Category: Edwards~~, A M~~]]	+	[[Category: Ehn M]]
-	[[Category: Ehn, M]]	+	[[Category: Flodin S]]
-	[[Category: Flodin, S]]	+	[[Category: Flores A]]
-	[[Category: Flores, A]]	+	[[Category: Graslund S]]
-	[[Category: Graslund, S]]	+	[[Category: Hallberg BM]]
-	[[Category: Hallberg~~, B M~~]]	+	[[Category: Hammarstrom M]]
-	[[Category: Hammarstrom, M]]	+	[[Category: Hogbom M]]
-	[[Category: Hogbom, M]]	+	[[Category: Holmberg-Schiavone L]]
-	[[Category: Holmberg-Schiavone, L]]	+	[[Category: Kotenyova T]]
-	[[Category: Kotenyova, T]]	+	[[Category: Lehtio L]]
-	[[Category: Lehtio, L]]	+	[[Category: Nilsson-Ehle P]]
-	[[Category: Nilsson-Ehle, P]]	+	[[Category: Nordlund P]]
-	[[Category: Nordlund, P]]	+	[[Category: Nyman T]]
-	[[Category: Nyman, T]]	+	[[Category: Ogg D]]
-	[[Category: Ogg, D]]	+	[[Category: Persson C]]
-	[[Category: Persson, C]]	+	[[Category: Sagemark J]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Stenmark P]]
-	[[Category: Sagemark, J]]	+	[[Category: Sundstrom M]]
-	[[Category: Stenmark, P]]	+	[[Category: Thorsell AG]]
-	[[Category: Sundstrom, M]]	+	[[Category: Uppenberg J]]
-	[[Category: Thorsell~~, A G~~]]	+	[[Category: Van den Berg S]]
-	[[Category: Uppenberg, J]]	+	[[Category: Weigelt J]]
-	[[Category: ~~Weigelt, J~~]]	+
-	[[Category: ~~Alternative initiation]]~~	+
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Developmental protein]]~~	+
-	~~[[Category: Differentiation]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mrna transport]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phosphorylation]]~~	+
-	~~[[Category: Rna helicase]]~~	+
-	~~[[Category: Rna-binding]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Sgc]]~~	+
-	~~[[Category: Spermatogenesis]]~~	+
-	~~[[Category: Translation regulation]]~~	+
-	~~[[Category: Transport~~]]	+

OCA at 04:20, 2 July 2021

OCA — Fri, 02 Jul 2021 04:20:17 GMT

←Older revision		Revision as of 04:20, 2 July 2021
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	==Crystal structure of the Helicase domain of human DDX25 RNA helicase==		==Crystal structure of the Helicase domain of human DDX25 RNA helicase==
-	<StructureSection load='2rb4' size='340' side='right' caption='[[2rb4]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='2rb4' size='340' side='right'caption='[[2rb4]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rb4]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RB4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rb4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RB4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDX25, GRTH ([~~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">DDX25, GRTH ([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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2rb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb4 OCA], [~~http~~://pdbe.org/2rb4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rb4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rb4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rb4 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=2rb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb4 OCA], [https://pdbe.org/2rb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rb4 RCSB], [https://www.ebi.ac.uk/pdbsum/2rb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rb4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DDX25_HUMAN DDX25_HUMAN]] ATP-dependent RNA helicase. Required for mRNA export and translation regulation during spermatid development (By similarity).<ref>PMID:10608860</ref>	+	[[https://www.uniprot.org/uniprot/DDX25_HUMAN DDX25_HUMAN]] ATP-dependent RNA helicase. Required for mRNA export and translation regulation during spermatid development (By similarity).<ref>PMID:10608860</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rb/2rb4_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rb/2rb4_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 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2rb4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2rb4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Helicase 3D structures\|Helicase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Berg, S Van den]]		[[Category: Berg, S Van den]]

OCA at 08:14, 12 October 2017

OCA — Thu, 12 Oct 2017 08:14:25 GMT

←Older revision		Revision as of 08:14, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of the Helicase domain of human DDX25 RNA helicase==		==Crystal structure of the Helicase domain of human DDX25 RNA helicase==
	<StructureSection load='2rb4' size='340' side='right' caption='[[2rb4]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2rb4' size='340' side='right' caption='[[2rb4]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDX25, GRTH ([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">DDX25, GRTH ([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=2rb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb4 OCA], [http://pdbe.org/2rb4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rb4 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb4 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=2rb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb4 OCA], [http://pdbe.org/2rb4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rb4 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rb4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2rb4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2rb4" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Helicase\|Helicase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:43, 10 February 2016

OCA — Wed, 10 Feb 2016 02:43:22 GMT

←Older revision		Revision as of 02:43, 10 February 2016
Line 2:		Line 2:
	<StructureSection load='2rb4' size='340' side='right' caption='[[2rb4]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2rb4' size='340' side='right' caption='[[2rb4]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rb4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RB4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rb4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RB4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDX25, GRTH ([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">DDX25, GRTH ([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=2rb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rb4 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb4 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=2rb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb4 OCA], [http://pdbe.org/2rb4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rb4 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb4 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=2rb4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 2rb4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Berg, S Van den]]		[[Category: Berg, S Van den]]

OCA at 11:13, 25 December 2014

OCA — Thu, 25 Dec 2014 11:13:57 GMT

←Older revision		Revision as of 11:13, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rb4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RB4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rb4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RB4 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDX25, GRTH ([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">DDX25, GRTH ([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=2rb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rb4 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb4 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=2rb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rb4 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb4 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DDX25_HUMAN DDX25_HUMAN]] ATP-dependent RNA helicase. Required for mRNA export and translation regulation during spermatid development (By similarity).<ref>PMID:10608860</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Arrowsmith, C H.]]	+	[[Category: Arrowsmith, C H]]
-	[[Category: Berg, S Van den.]]	+	[[Category: Berg, S Van den]]
-	[[Category: Berglund, H.]]	+	[[Category: Berglund, H]]
-	[[Category: Edwards, A M.]]	+	[[Category: Edwards, A M]]
-	[[Category: Ehn, M.]]	+	[[Category: Ehn, M]]
-	[[Category: Flodin, S.]]	+	[[Category: Flodin, S]]
-	[[Category: Flores, A.]]	+	[[Category: Flores, A]]
-	[[Category: Graslund, S.]]	+	[[Category: Graslund, S]]
-	[[Category: Hallberg, B M.]]	+	[[Category: Hallberg, B M]]
-	[[Category: Hammarstrom, M.]]	+	[[Category: Hammarstrom, M]]
-	[[Category: Hogbom, M.]]	+	[[Category: Hogbom, M]]
-	[[Category: Holmberg-Schiavone, L.]]	+	[[Category: Holmberg-Schiavone, L]]
-	[[Category: Kotenyova, T.]]	+	[[Category: Kotenyova, T]]
-	[[Category: Lehtio, L.]]	+	[[Category: Lehtio, L]]
-	[[Category: Nilsson-Ehle, P.]]	+	[[Category: Nilsson-Ehle, P]]
-	[[Category: Nordlund, P.]]	+	[[Category: Nordlund, P]]
-	[[Category: Nyman, T.]]	+	[[Category: Nyman, T]]
-	[[Category: Ogg, D.]]	+	[[Category: Ogg, D]]
-	[[Category: Persson, C.]]	+	[[Category: Persson, C]]
-	[[Category: ~~SGC,~~ Structural ~~Genomics Consortium.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sagemark, J.]]	+	[[Category: Sagemark, J]]
-	[[Category: Stenmark, P.]]	+	[[Category: Stenmark, P]]
-	[[Category: Sundstrom, M.]]	+	[[Category: Sundstrom, M]]
-	[[Category: Thorsell, A G.]]	+	[[Category: Thorsell, A G]]
-	[[Category: Uppenberg, J.]]	+	[[Category: Uppenberg, J]]
-	[[Category: Weigelt, J.]]	+	[[Category: Weigelt, J]]
	[[Category: Alternative initiation]]		[[Category: Alternative initiation]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
Line 73:		Line 75:
	[[Category: Sgc]]		[[Category: Sgc]]
	[[Category: Spermatogenesis]]		[[Category: Spermatogenesis]]
-	[[Category: Structural genomic]]
-	[[Category: Structural genomics consortium]]
	[[Category: Translation regulation]]		[[Category: Translation regulation]]
	[[Category: Transport]]		[[Category: Transport]]

OCA at 06:26, 29 September 2014

OCA — Mon, 29 Sep 2014 06:26:04 GMT

←Older revision		Revision as of 06:26, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2rb4.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the Helicase domain of human DDX25 RNA helicase==
		+	<StructureSection load='2rb4' size='340' side='right' caption='[[2rb4]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2rb4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RB4 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDX25, GRTH ([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=2rb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rb4 RCSB], [http://www.ebi.ac.uk/pdbsum/2rb4 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/rb/2rb4_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 ==
		+	DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.

-	~~{{STRUCTURE_2rb4\| PDB=2rb4 \| SCENE= }}~~	+	Comparative structural analysis of human DEAD-box RNA helicases.,Schutz P, Karlberg T, van den Berg S, Collins R, Lehtio L, Hogbom M, Holmberg-Schiavone L, Tempel W, Park HW, Hammarstrom M, Moche M, Thorsell AG, Schuler H PLoS One. 2010 Sep 30;5(9). pii: e12791. PMID:20941364<ref>PMID:20941364</ref>

-	~~===Crystal structure~~ of the ~~Helicase domain of human DDX25 RNA helicase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20941364}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2rb4]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~This structure supersedes the now removed PDB entry [http:~~/~~/oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA].~~	+

	==See Also==		==See Also==
	*[[Helicase\|Helicase]]		*[[Helicase\|Helicase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020941364<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Arrowsmith, C H.]]		[[Category: Arrowsmith, C H.]]

OCA at 16:03, 20 October 2012

OCA — Sat, 20 Oct 2012 16:03:01 GMT

←Older revision		Revision as of 16:03, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2rb4]] is a 2 chain structure ~~of [[Helicase]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA].	+	[[2rb4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA].

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

OCA: Protected "2rb4" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 20:25:33 GMT

Protected "2rb4" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:25, 26 July 2012

OCA at 20:25, 26 July 2012

OCA — Thu, 26 Jul 2012 20:25:31 GMT

←Older revision		Revision as of 20:25, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2rb4.png\|left\|200px]]		[[Image:2rb4.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2rb4", 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_2rb4\| PDB=2rb4 \| SCENE= }}		{{STRUCTURE_2rb4\| PDB=2rb4 \| SCENE= }}

	===Crystal structure of the Helicase domain of human DDX25 RNA helicase===		===Crystal structure of the Helicase domain of human DDX25 RNA helicase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20941364}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20941364 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20941364}}		{{ABSTRACT_PUBMED_20941364}}

	==About this Structure==		==About this Structure==
-	~~2RB4~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA].	+	[[2rb4]] is a 2 chain structure of [[Helicase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA].
		+
		+	==See Also==
		+	*[[Helicase\|Helicase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20941364~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020941364</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Arrowsmith, C H.]]		[[Category: Arrowsmith, C H.]]
Line 69:		Line 60:
	[[Category: Translation regulation]]		[[Category: Translation regulation]]
	[[Category: Transport]]		[[Category: Transport]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 27 11:41:19 2010''

OCA at 08:30, 27 October 2010

OCA — Wed, 27 Oct 2010 08:30:56 GMT

←Older revision		Revision as of 08:30, 27 October 2010
Line 12:		Line 12:
	===Crystal structure of the Helicase domain of human DDX25 RNA helicase===		===Crystal structure of the Helicase domain of human DDX25 RNA helicase===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20941364}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20941364 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20941364}}

	==About this Structure==		==About this Structure==
-	2RB4 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA].	+	2RB4 is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g2j 2g2j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB4 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20941364</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Arrowsmith, C H.]]		[[Category: Arrowsmith, C H.]]
Line 44:		Line 53:
	[[Category: Alternative initiation]]		[[Category: Alternative initiation]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
-	[[Category: Cytoplasm]]
	[[Category: Developmental protein]]		[[Category: Developmental protein]]
	[[Category: Differentiation]]		[[Category: Differentiation]]
Line 62:		Line 70:
	[[Category: Transport]]		[[Category: Transport]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Feb 17 14~~:46:~~17 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 27 11:41:19 2010''