4dwl - Revision history

OCA at 08:41, 21 September 2022

OCA — Wed, 21 Sep 2022 08:41:36 GMT

←Older revision		Revision as of 08:41, 21 September 2022
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	==Avd molecule from Bordetella bacteriophage DGR==		==Avd molecule from Bordetella bacteriophage DGR==
-	<StructureSection load='4dwl' size='340' side='right' caption='[[4dwl]], [[Resolution\|resolution]] 2.69Å' scene=''>	+	<StructureSection load='4dwl' size='340' side='right'caption='[[4dwl]], [[Resolution\|resolution]] 2.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dwl]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpbpp Bpbpp~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DWL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DWL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dwl]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bordetella_virus_BPP1 Bordetella virus BPP1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DWL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DWL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"~~><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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr~~ id~~='NonStdRes'><td class~~="~~sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat~~"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4dwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dwl OCA], [https://pdbe.org/4dwl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dwl RCSB], [https://www.ebi.ac.uk/pdbsum/4dwl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dwl ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">bbp7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=194699 BPBPP])~~</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=4dwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dwl OCA], [~~http~~://pdbe.org/4dwl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4dwl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4dwl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4dwl ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/Q775D7_BPBPP Q775D7_BPBPP]]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpbpp~~]]	+	[[Category: Bordetella virus BPP1]]
-	[[Category: ~~Al-Ayyoubi, M~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ghosh, P~~]]	+	[[Category: Al-Ayyoubi M]]
-	[[Category: ~~Accessory variability determinant from bordetella bacteriophage diversity generating retroelement]]~~	+	[[Category: Ghosh P]]
-	~~[[Category: Nucleic acid binding protein]]~~	+
-	~~[[Category: Pentameric four helix bundle]]~~	+
-	~~[[Category: Phosphate binding protein]]~~	+
-	~~[[Category: Reverse transcriptase~~]]	+

OCA at 10:58, 11 August 2016

OCA — Thu, 11 Aug 2016 10:58:08 GMT

←Older revision		Revision as of 10:58, 11 August 2016
Line 1:		Line 1:
		+
	==Avd molecule from Bordetella bacteriophage DGR==		==Avd molecule from Bordetella bacteriophage DGR==
	<StructureSection load='4dwl' size='340' side='right' caption='[[4dwl]], [[Resolution\|resolution]] 2.69Å' scene=''>		<StructureSection load='4dwl' size='340' side='right' caption='[[4dwl]], [[Resolution\|resolution]] 2.69Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bbp7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=194699 BPBPP])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bbp7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=194699 BPBPP])</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=4dwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dwl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dwl RCSB], [http://www.ebi.ac.uk/pdbsum/4dwl 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=4dwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dwl OCA], [http://pdbe.org/4dwl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dwl RCSB], [http://www.ebi.ac.uk/pdbsum/4dwl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dwl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4dwl" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:03, 14 January 2015

OCA — Wed, 14 Jan 2015 08:03:10 GMT

←Older revision		Revision as of 08:03, 14 January 2015
Line 2:		Line 2:
	<StructureSection load='4dwl' size='340' side='right' caption='[[4dwl]], [[Resolution\|resolution]] 2.69Å' scene=''>		<StructureSection load='4dwl' size='340' side='right' caption='[[4dwl]], [[Resolution\|resolution]] 2.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dwl]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bordetella_phage_bpp-1 Bordetella phage bpp-1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DWL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DWL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dwl]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpbpp Bpbpp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DWL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DWL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bbp7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=194699 ~~Bordetella phage BPP-1~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bbp7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=194699 BPBPP])</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=4dwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dwl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dwl RCSB], [http://www.ebi.ac.uk/pdbsum/4dwl 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=4dwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dwl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dwl RCSB], [http://www.ebi.ac.uk/pdbsum/4dwl PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Diversity-generating retroelements (DGRs) are the only known source of massive protein sequence variation in prokaryotes. These elements transfer coding information from a template region (TR) through an RNA intermediate to a protein-encoding variable region. This retrohoming process is accompanied by unique adenine-specific mutagenesis and, in the prototypical BPP-1 DGR, requires a reverse transcriptase (bRT) and an accessory variability determinant (bAvd) protein. To understand the role of bAvd, we determined its 2.69 A resolution structure, which revealed a highly positively charged pentameric barrel. In accordance with its charge, bAvd bound both DNA and RNA, albeit without a discernable sequence preference. We found that the coding sequence of bAvd functioned as part of TR but identified means to mutate bAvd without affecting TR. This mutational analysis revealed a strict correspondence between retrohoming and interaction of bAvd with bRT, suggesting that the bRT-bAvd complex is important for DGR retrohoming.
		+
		+	Structure of the essential diversity-generating retroelement protein bAvd and its functionally important interaction with reverse transcriptase.,Alayyoubi M, Guo H, Dey S, Golnazarian T, Brooks GA, Rong A, Miller JF, Ghosh P Structure. 2013 Feb 5;21(2):266-76. doi: 10.1016/j.str.2012.11.016. Epub 2012 Dec, 27. PMID:23273427<ref>PMID:23273427</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bordetella phage bpp-1~~]]	+	[[Category: Bpbpp]]
	[[Category: Al-Ayyoubi, M]]		[[Category: Al-Ayyoubi, M]]
	[[Category: Ghosh, P]]		[[Category: Ghosh, P]]

OCA at 12:41, 4 January 2015

OCA — Sun, 04 Jan 2015 12:41:23 GMT

←Older revision		Revision as of 12:41, 4 January 2015
Line 1:		Line 1:
-	~~[[Image:4dwl.jpg\|left\|200px]]~~	+	==Avd molecule from Bordetella bacteriophage DGR==
-		+	<StructureSection load='4dwl' size='340' side='right' caption='[[4dwl]], [[Resolution\|resolution]] 2.69Å' scene=''>
-	~~{{STRUCTURE_4dwl\| PDB=4dwl \| SCENE= }}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4dwl]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bordetella_phage_bpp-1 Bordetella phage bpp-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DWL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DWL FirstGlance]. <br>
-	===Avd molecule from Bordetella bacteriophage DGR===	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bbp7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=194699 Bordetella phage BPP-1])</td></tr>
-	==~~About this Structure~~==	+	<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=4dwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dwl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dwl RCSB], [http://www.ebi.ac.uk/pdbsum/4dwl PDBsum]</span></td></tr>
-	[[4dwl]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bordetella_phage_bpp-1 Bordetella phage bpp-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DWL OCA].	+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bordetella phage bpp-1]]		[[Category: Bordetella phage bpp-1]]
-	[[Category: Al-Ayyoubi, M.]]	+	[[Category: Al-Ayyoubi, M]]
-	[[Category: Ghosh, P.]]	+	[[Category: Ghosh, P]]
	[[Category: Accessory variability determinant from bordetella bacteriophage diversity generating retroelement]]		[[Category: Accessory variability determinant from bordetella bacteriophage diversity generating retroelement]]
	[[Category: Nucleic acid binding protein]]		[[Category: Nucleic acid binding protein]]

OCA at 14:55, 27 February 2013

OCA — Wed, 27 Feb 2013 14:55:53 GMT

←Older revision		Revision as of 14:55, 27 February 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4dwl.jpg\|left\|200px]]

-	~~The entry~~ 4dwl ~~is ON HOLD~~ ~~until Feb 27 2014~~	+	{{STRUCTURE_4dwl\| PDB=4dwl \| SCENE= }}

-	~~Authors: Ghosh, P., Al-Ayyoubi, M.~~	+	===Avd molecule from Bordetella bacteriophage DGR===

-	~~Description~~: ~~Avd molecule~~ from Bordetella bacteriophage ~~DGR~~	+
		+	==About this Structure==
		+	[[4dwl]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bordetella_phage_bpp-1 Bordetella phage bpp-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DWL OCA].
		+	[[Category: Bordetella phage bpp-1]]
		+	[[Category: Al-Ayyoubi, M.]]
		+	[[Category: Ghosh, P.]]
		+	[[Category: Accessory variability determinant from bordetella bacteriophage diversity generating retroelement]]
		+	[[Category: Nucleic acid binding protein]]
		+	[[Category: Pentameric four helix bundle]]
		+	[[Category: Phosphate binding protein]]
		+	[[Category: Reverse transcriptase]]

OCA at 07:41, 9 January 2013

OCA — Wed, 09 Jan 2013 07:41:00 GMT

←Older revision		Revision as of 07:41, 9 January 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4dwl is ON HOLD until ~~Paper Publication~~	+	The entry 4dwl is ON HOLD until Feb 27 2014

	Authors: Ghosh, P., Al-Ayyoubi, M.		Authors: Ghosh, P., Al-Ayyoubi, M.

	Description: Avd molecule from Bordetella bacteriophage DGR		Description: Avd molecule from Bordetella bacteriophage DGR

OCA at 05:23, 30 May 2012

OCA — Wed, 30 May 2012 05:23:48 GMT

←Older revision		Revision as of 05:23, 30 May 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4dwl is ON HOLD	+	The entry 4dwl is ON HOLD until Paper Publication

	Authors: Ghosh, P., Al-Ayyoubi, M.		Authors: Ghosh, P., Al-Ayyoubi, M.

	Description: Avd molecule from Bordetella bacteriophage DGR		Description: Avd molecule from Bordetella bacteriophage DGR

OCA: Protected "4dwl" [edit=sysop:move=sysop]

OCA — Thu, 08 Mar 2012 05:27:46 GMT

Protected "4dwl" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:27, 8 March 2012

OCA: New page: '''Unreleased structure''' The entry 4dwl is ON HOLD Authors: Ghosh, P., Al-Ayyoubi, M. Description: Avd molecule from Bordetella bacteriophage DGR

OCA — Thu, 08 Mar 2012 05:27:45 GMT

New page: '''Unreleased structure''' The entry 4dwl is ON HOLD Authors: Ghosh, P., Al-Ayyoubi, M. Description: Avd molecule from Bordetella bacteriophage DGR

New page

'''Unreleased structure'''

The entry 4dwl is ON HOLD

Authors: Ghosh, P., Al-Ayyoubi, M.

Description: Avd molecule from Bordetella bacteriophage DGR