6w7t - Revision history

OCA at 14:18, 18 October 2023

OCA — Wed, 18 Oct 2023 14:18:18 GMT

←Older revision		Revision as of 14:18, 18 October 2023
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	<StructureSection load='6w7t' size='340' side='right'caption='[[6w7t]], [[Resolution\|resolution]] 3.01Å' scene=''>		<StructureSection load='6w7t' size='340' side='right'caption='[[6w7t]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6w7t]] is a 9 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseudomonas_aeruginosa_phage_pap3~~ Pseudomonas ~~aeruginosa phage pap3~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W7T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6W7T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w7t]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_virus_PaP3 Pseudomonas virus PaP3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6W7T FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[3zqp\|3zqp]]</div></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.01Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">orf1 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=188350 Pseudomonas aeruginosa phage PaP3])~~</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=6w7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w7t OCA], [https://pdbe.org/6w7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6w7t RCSB], [https://www.ebi.ac.uk/pdbsum/6w7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6w7t 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=6w7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w7t OCA], [~~http~~://pdbe.org/6w7t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6w7t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6w7t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6w7t ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8H9R5_9CAUD Q8H9R5_9CAUD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Terminase\|Terminase]]	+	*[[Terminase 3D Structures\|Terminase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pseudomonas ~~aeruginosa phage pap3~~]]	+	[[Category: Pseudomonas virus PaP3]]
-	[[Category: Cingolani, G]]	+	[[Category: Cingolani G]]
-	[[Category: Lokareddy, R]]	+	[[Category: Lokareddy R]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Pseudomonas phage pap3]]~~	+
-	~~[[Category: Small terminase]]~~	+
-	~~[[Category: Viral genome packaging motor]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 07:10, 25 November 2020

OCA — Wed, 25 Nov 2020 07:10:24 GMT

←Older revision		Revision as of 07:10, 25 November 2020
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	==Structure of PaP3 small terminase==		==Structure of PaP3 small terminase==
-	<StructureSection load='6w7t' size='340' side='right'caption='[[6w7t]]' scene=''>	+	<StructureSection load='6w7t' size='340' side='right'caption='[[6w7t]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W7T OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W7T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w7t]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_phage_pap3 Pseudomonas aeruginosa phage pap3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W7T OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W7T FirstGlance]. <br>
-	</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=6w7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w7t OCA], [http://pdbe.org/6w7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w7t RCSB], [http://www.ebi.ac.uk/pdbsum/6w7t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w7t ProSAT]</span></td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3zqp\|3zqp]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">orf1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=188350 Pseudomonas aeruginosa phage PaP3])</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=6w7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w7t OCA], [http://pdbe.org/6w7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w7t RCSB], [http://www.ebi.ac.uk/pdbsum/6w7t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w7t ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The genome packaging motor of tailed bacteriophages and herpesviruses is a powerful nanomachine built by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal vertex of an empty precursor capsid (or procapsid) to power genome encapsidation. Terminase subunits have been studied in-depth, especially in classical bacteriophages that infect Escherichia coli or Salmonella, yet, less is known about the packaging motor of Pseudomonas-phages that have increasing biomedical relevance. Here, we investigated the small terminase subunit from three Podoviridae phages that infect Pseudomonas aeruginosa. We found TerS is polymorphic in solution but assembles into a nonamer in its high-affinity heparin-binding conformation. The atomic structure of Pseudomonas phage PaP3 TerS, the first complete structure for a TerS from a cos phage, reveals nine helix-turn-helix (HTH) motifs asymmetrically arranged around a beta-stranded channel, too narrow to accommodate DNA. PaP3 TerS binds DNA in a sequence-specific manner in vitro. X-ray scattering and molecular modeling suggest TerS adopts an open conformation in solution, characterized by dynamic HTHs that move around an oligomerization core, generating discrete binding crevices for DNA. We propose a model for sequence-specific recognition of packaging initiation sites by lateral interdigitation of DNA.
		+
		+	Biophysical analysis of Pseudomonas-phage PaP3 small terminase suggests a mechanism for sequence-specific DNA-binding by lateral interdigitation.,Niazi M, Florio TJ, Yang R, Lokareddy RK, Swanson NA, Gillilan RE, Cingolani G Nucleic Acids Res. 2020 Oct 30. pii: 5943822. doi: 10.1093/nar/gkaa866. PMID:33125059<ref>PMID:33125059</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6w7t" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Terminase\|Terminase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cingolani G]]	+	[[Category: Pseudomonas aeruginosa phage pap3]]
-	[[Category: Lokareddy R]]	+	[[Category: Cingolani, G]]
		+	[[Category: Lokareddy, R]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Pseudomonas phage pap3]]
		+	[[Category: Small terminase]]
		+	[[Category: Viral genome packaging motor]]
		+	[[Category: Viral protein]]

OCA at 07:59, 11 November 2020

OCA — Wed, 11 Nov 2020 07:59:35 GMT

←Older revision		Revision as of 07:59, 11 November 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6w7t ~~is ON HOLD until Mar 19 2022~~	+	==Structure of PaP3 small terminase==
-		+	<StructureSection load='6w7t' size='340' side='right'caption='[[6w7t]]' scene=''>
-	~~Authors~~: ~~Cingolani~~, G., ~~Lokareddy~~, R.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W7T OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W7T FirstGlance]. <br>
-	~~Description: Structure of PaP3 small terminase~~	+	</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=6w7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w7t OCA], [http://pdbe.org/6w7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w7t RCSB], [http://www.ebi.ac.uk/pdbsum/6w7t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w7t ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Cingolani, G]]	+	__TOC__
-	[[Category: Lokareddy, R]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cingolani G]]
		+	[[Category: Lokareddy R]]

OCA at 03:58, 13 May 2020

OCA — Wed, 13 May 2020 03:58:05 GMT

←Older revision		Revision as of 03:58, 13 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6w7t is ON HOLD	+	The entry 6w7t is ON HOLD until Mar 19 2022

	Authors: Cingolani, G., Lokareddy, R.		Authors: Cingolani, G., Lokareddy, R.

OCA: Protected "6w7t" [edit=sysop:move=sysop]

OCA — Fri, 27 Mar 2020 08:30:04 GMT

Protected "6w7t" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:30, 27 March 2020

OCA: New page: '''Unreleased structure''' The entry 6w7t is ON HOLD Authors: Cingolani, G., Lokareddy, R. Description: Structure of PaP3 small terminase Category: Unreleased Structures [[Category...

OCA — Fri, 27 Mar 2020 08:30:03 GMT

New page: '''Unreleased structure''' The entry 6w7t is ON HOLD Authors: Cingolani, G., Lokareddy, R. Description: Structure of PaP3 small terminase Category: Unreleased Structures [[Category...

New page

'''Unreleased structure'''

The entry 6w7t is ON HOLD

Authors: Cingolani, G., Lokareddy, R.

Description: Structure of PaP3 small terminase
[[Category: Unreleased Structures]]
[[Category: Cingolani, G]]
[[Category: Lokareddy, R]]