1u0j - Revision history

OCA at 06:36, 23 August 2023

OCA — Wed, 23 Aug 2023 06:36:03 GMT

←Older revision		Revision as of 06:36, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='1u0j' size='340' side='right'caption='[[1u0j]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1u0j' size='340' side='right'caption='[[1u0j]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u0j]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aav~~-~~2 Aav~~-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1U0J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u0j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Adeno-associated_virus_2 Adeno-associated virus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U0J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADP:ADENOSINE~~-~~5-DIPHOSPHATE'>ADP</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]] 2.1Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~REP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=10804 AAV~~-~~2])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></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=1u0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u0j OCA], [~~http~~://pdbe.org/1u0j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1u0j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1u0j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1u0j 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=1u0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u0j OCA], [https://pdbe.org/1u0j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u0j RCSB], [https://www.ebi.ac.uk/pdbsum/1u0j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u0j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/REP68_AAV2S REP68_AAV2S] Plays an essential role in the initiation of viral DNA synthesis. Binds specifically to an inverted terminal repeat element (ITR) on the 3' and 5' ends of the viral DNA, where it cleaves a site specifically to generate a priming site for initiation of the synthesis of a complementary strand. Plays also a role as transcriptional regulator, DNA helicase and as key factor in site-specific integration of the viral genome. Inhibits the host cell cycle G1/S and G2/M transitions. These arrests may provide essential cellular factors for viral DNA replication.<ref>PMID:9882364</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aav~~-2]]	+	[[Category: Adeno-associated virus 2]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aggarwal~~, A K~~]]	+	[[Category: Aggarwal AK]]
-	[[Category: Escalante~~, C R~~]]	+	[[Category: Escalante CR]]
-	[[Category: James~~, J A~~]]	+	[[Category: James JA]]
-	[[Category: Linden~~, R M]]~~	+	[[Category: Linden RM]]
-	~~[[Category: Aaa+ protein]]~~	+
-	~~[[Category: Helicase]]~~	+
-	~~[[Category: P-loop atpase]]~~	+
-	~~[[Category: Replication~~]]	+

OCA at 07:17, 30 December 2020

OCA — Wed, 30 Dec 2020 07:17:50 GMT

←Older revision		Revision as of 07:17, 30 December 2020
Line 1:		Line 1:

	==Crystal Structure of AAV2 Rep40-ADP complex==		==Crystal Structure of AAV2 Rep40-ADP complex==
-	<StructureSection load='1u0j' size='340' side='right' caption='[[1u0j]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1u0j' size='340' side='right'caption='[[1u0j]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aav-2 Aav-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0J OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1U0J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aav-2 Aav-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1U0J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">REP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10804 AAV-2])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">REP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10804 AAV-2])</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=1u0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u0j OCA], [http://pdbe.org/1u0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u0j RCSB], [http://www.ebi.ac.uk/pdbsum/1u0j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u0j 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=1u0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u0j OCA], [http://pdbe.org/1u0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u0j RCSB], [http://www.ebi.ac.uk/pdbsum/1u0j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u0j ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</StructureSection>		</StructureSection>
	[[Category: Aav-2]]		[[Category: Aav-2]]
		+	[[Category: Large Structures]]
	[[Category: Aggarwal, A K]]		[[Category: Aggarwal, A K]]
	[[Category: Escalante, C R]]		[[Category: Escalante, C R]]

OCA at 06:32, 31 January 2018

OCA — Wed, 31 Jan 2018 06:32:57 GMT

←Older revision		Revision as of 06:32, 31 January 2018
Line 1:		Line 1:
		+
	==Crystal Structure of AAV2 Rep40-ADP complex==		==Crystal Structure of AAV2 Rep40-ADP complex==
	<StructureSection load='1u0j' size='340' side='right' caption='[[1u0j]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1u0j' size='340' side='right' caption='[[1u0j]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">REP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10804 AAV-2])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">REP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10804 AAV-2])</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=1u0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u0j OCA], [http://pdbe.org/1u0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u0j RCSB], [http://www.ebi.ac.uk/pdbsum/1u0j 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=1u0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u0j OCA], [http://pdbe.org/1u0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u0j RCSB], [http://www.ebi.ac.uk/pdbsum/1u0j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u0j ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u0/1u0j_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u0/1u0j_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 07:24, 9 February 2016

OCA — Tue, 09 Feb 2016 07:24:05 GMT

←Older revision		Revision as of 07:24, 9 February 2016
Line 15:		Line 15:
	<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=1u0j ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:56, 10 September 2015

OCA — Thu, 10 Sep 2015 19:56:29 GMT

←Older revision		Revision as of 19:56, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1u0j' size='340' side='right' caption='[[1u0j]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1u0j' size='340' side='right' caption='[[1u0j]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Adeno~~-~~associated_virus_-_2 Adeno-associated virus~~ - 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U0J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aav-2 Aav-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U0J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">REP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10804 ~~Adeno-associated virus~~ - 2])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">REP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10804 AAV-2])</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=1u0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u0j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u0j RCSB], [http://www.ebi.ac.uk/pdbsum/1u0j 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=1u0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u0j OCA], [http://pdbe.org/1u0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u0j RCSB], [http://www.ebi.ac.uk/pdbsum/1u0j PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1u0j" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Adeno-associated virus~~ - 2]]	+	[[Category: Aav-2]]
	[[Category: Aggarwal, A K]]		[[Category: Aggarwal, A K]]
	[[Category: Escalante, C R]]		[[Category: Escalante, C R]]

OCA at 13:24, 6 January 2015

OCA — Tue, 06 Jan 2015 13:24:31 GMT

←Older revision		Revision as of 13:24, 6 January 2015
Line 1:		Line 1:
-	[[~~Image:~~1u0j.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of AAV2 Rep40-ADP complex==
		+	<StructureSection load='1u0j' size='340' side='right' caption='[[1u0j]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1u0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Adeno-associated_virus_-_2 Adeno-associated virus - 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U0J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">REP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10804 Adeno-associated virus - 2])</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=1u0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u0j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u0j RCSB], [http://www.ebi.ac.uk/pdbsum/1u0j 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/u0/1u0j_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 ==
		+	We have determined the structure of adeno-associated virus type 2 (AAV2) Rep40 to 2.1-A resolution with ADP bound at the active site. The complex crystallizes as a monomer with one ADP molecule positioned in an unexpectedly open binding site. The nucleotide-binding pocket consists of the P-loop residues interacting with the phosphates and a loop (nucleoside-binding loop) that emanates from the last strand of the central beta-sheet and interacts with the sugar and base. As a result of the open nature of the binding site, one face of the adenine ring is completely exposed to the solvent, and consequently the number of protein-nucleotide contacts is scarce as compared with other P-loop nucleotide phosphohydrolases. The conformation of the ADP molecule in its binding site bears a resemblance to those found in only three other families of P-loop ATPases: the ATP-binding cassette transporter family, the bacterial RecA proteins, and the type II topoisomerase family. In all these cases, oligomerization is required to attain a competent nucleotide-binding pocket. We propose that this characteristic is native to superfamily 3 helicases and allows for an additional mechanism of regulation by these multifunctional proteins. Furthermore, it explains the strong tendency by members of this family such as simian virus 40 TAg to oligomerize after binding ATP.

-	~~{{STRUCTURE_1u0j\| PDB=1u0j \| SCENE= }}~~	+	Structure of adeno-associated virus type 2 Rep40-ADP complex: insight into nucleotide recognition and catalysis by superfamily 3 helicases.,James JA, Aggarwal AK, Linden RM, Escalante CR Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12455-60. Epub 2004 Aug 13. PMID:15310852<ref>PMID:15310852</ref>

-	~~===Crystal Structure~~ of ~~AAV2 Rep40-ADP complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15310852}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1u0j]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Adeno-associated_virus_-_2 Adeno-associated virus - 2]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1U0J OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015310852<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Adeno-associated virus - 2]]		[[Category: Adeno-associated virus - 2]]
-	[[Category: Aggarwal, A K.]]	+	[[Category: Aggarwal, A K]]
-	[[Category: Escalante, C R.]]	+	[[Category: Escalante, C R]]
-	[[Category: James, J A.]]	+	[[Category: James, J A]]
-	[[Category: Linden, R M.]]	+	[[Category: Linden, R M]]
	[[Category: Aaa+ protein]]		[[Category: Aaa+ protein]]
	[[Category: Helicase]]		[[Category: Helicase]]
	[[Category: P-loop atpase]]		[[Category: P-loop atpase]]
	[[Category: Replication]]		[[Category: Replication]]

OCA: Protected "1u0j" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 11:42:59 GMT

Protected "1u0j" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:42, 5 January 2013

OCA at 11:42, 5 January 2013

OCA — Sat, 05 Jan 2013 11:42:54 GMT

←Older revision		Revision as of 11:42, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1u0j.png\|left\|200px]]		[[Image:1u0j.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1u0j", 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_1u0j\| PDB=1u0j \| SCENE= }}		{{STRUCTURE_1u0j\| PDB=1u0j \| SCENE= }}

	===Crystal Structure of AAV2 Rep40-ADP complex===		===Crystal Structure of AAV2 Rep40-ADP complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15310852}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15310852 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_15310852}}		{{ABSTRACT_PUBMED_15310852}}

	==About this Structure==		==About this Structure==
-	~~1U0J~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Adeno-~~associated_virus_2~~ Adeno-associated virus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0J OCA].	+	[[1u0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Adeno-associated_virus_-_2 Adeno-associated virus - 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0J OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15310852~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015310852</ref><references group="xtra"/>
-	[[Category: Adeno-associated virus 2]]	+	[[Category: Adeno-associated virus - 2]]
	[[Category: Aggarwal, A K.]]		[[Category: Aggarwal, A K.]]
	[[Category: Escalante, C R.]]		[[Category: Escalante, C R.]]
Line 32:		Line 20:
	[[Category: Helicase]]		[[Category: Helicase]]
	[[Category: P-loop atpase]]		[[Category: P-loop atpase]]
-		+	[[Category: Replication]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 07:56:25 2009''~~	+

OCA at 05:56, 17 February 2009

OCA — Tue, 17 Feb 2009 05:56:26 GMT

←Older revision		Revision as of 05:56, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1U0J is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Adeno-associated_virus_2 Adeno-associated virus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0J OCA].	+	1U0J is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Adeno-associated_virus_2 Adeno-associated virus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0J OCA].

	==Reference==		==Reference==
-	Structure of adeno-associated virus type 2 Rep40-ADP complex: insight into nucleotide recognition and catalysis by superfamily 3 helicases., James JA, Aggarwal AK, Linden RM, Escalante CR, Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12455-60. Epub 2004 Aug 13. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15310852 15310852]~~	+	<ref group="xtra">PMID:15310852</ref><references group="xtra"/>
	[[Category: Adeno-associated virus 2]]		[[Category: Adeno-associated virus 2]]
-	[[Category: Single protein]]
	[[Category: Aggarwal, A K.]]		[[Category: Aggarwal, A K.]]
	[[Category: Escalante, C R.]]		[[Category: Escalante, C R.]]
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	[[Category: P-loop atpase]]		[[Category: P-loop atpase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 11:~~17:~~42 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 07:56:25 2009''

OCA at 08:17, 28 July 2008

OCA — Mon, 28 Jul 2008 08:17:42 GMT

←Older revision		Revision as of 08:17, 28 July 2008
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-	[[Image:1u0j.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1u0j.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_1u0j\| PDB=1u0j \| SCENE= }}		{{STRUCTURE_1u0j\| PDB=1u0j \| SCENE= }}

-	~~'''~~Crystal Structure of AAV2 Rep40-ADP complex~~'''~~	+	===Crystal Structure of AAV2 Rep40-ADP complex===


-	~~==Overview==~~	+	<!--
-	~~We have determined~~ the ~~structure of adeno-associated virus type 2 (AAV2) Rep40~~ to ~~2.1-A resolution with ADP bound at~~ the ~~active site. The complex crystallizes~~ as ~~a monomer with one ADP molecule positioned in an unexpectedly open binding site~~. ~~The nucleotide-binding pocket consists of the P-loop residues interacting with the phosphates and a loop (nucleoside-binding loop~~) ~~that emanates from the last strand of the central beta-sheet and interacts with the sugar and base. As a result of the open nature of the binding site~~, ~~one face of the adenine ring~~ is ~~completely exposed to the solvent, and consequently~~ the number ~~of protein-nucleotide contacts is scarce as compared with other P-loop nucleotide phosphohydrolases~~. ~~The conformation of the ADP molecule in its binding site bears a resemblance to those found in only three other families of P~~-~~loop ATPases: the ATP~~-binding cassette transporter family, the bacterial RecA proteins, and the type II topoisomerase family. In all these cases, oligomerization is required to attain a competent nucleotide-binding pocket. We propose that this characteristic is native to superfamily 3 helicases and allows for an additional mechanism of regulation by these multifunctional proteins. Furthermore, it explains the strong tendency by members of this family such as simian virus 40 TAg to oligomerize after binding ATP.	+	The line below this paragraph, {{ABSTRACT_PUBMED_15310852}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 15310852 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_15310852}}

	==About this Structure==		==About this Structure==
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	[[Category: Helicase]]		[[Category: Helicase]]
	[[Category: P-loop atpase]]		[[Category: P-loop atpase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 10~~:36:06 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 11:17:42 2008''