5w5e - Revision history

OCA at 14:13, 13 March 2024

OCA — Wed, 13 Mar 2024 14:13:54 GMT

←Older revision		Revision as of 14:13, 13 March 2024
Line 3:		Line 3:
	<SX load='5w5e' size='340' side='right' viewer='molstar' caption='[[5w5e]], [[Resolution\|resolution]] 3.50Å' scene=''>		<SX load='5w5e' size='340' side='right' viewer='molstar' caption='[[5w5e]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w5e]] is a 30 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5W5E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w5e]] is a 30 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W5E FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[3j9q\|3j9q]]</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.5Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">FIIR2 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5&~~id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])~~</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=5w5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w5e OCA], [https://pdbe.org/5w5e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w5e RCSB], [https://www.ebi.ac.uk/pdbsum/5w5e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w5e 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=5w5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w5e OCA], [~~http~~://pdbe.org/5w5e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5w5e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5w5e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5w5e ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q9S573_PSEAI Q9S573_PSEAI]
-	R-type pyocins are representatives of contractile ejection systems, a class of biological nanomachines that includes, among others, the bacterial type VI secretion system (T6SS) and contractile bacteriophage tails. We report atomic models of the Pseudomonas aeruginosa precontraction pyocin sheath and tube, and the postcontraction sheath, obtained by cryo-EM at 3.5-A and 3.9-A resolutions, respectively. The central channel of the tube is negatively charged, in contrast to the neutral and positive counterparts in T6SSs and phage tails. The sheath is interwoven by long N- and C-terminal extension arms emanating from each subunit, which create an extensive two-dimensional mesh that has the same connectivity in the extended and contracted state of the sheath. We propose that the contraction process draws energy from electrostatic and shape complementarities to insert the inner tube through bacterial cell membranes to eventually kill the bacteria.	+
-		+
-	~~Atomic structures of a bactericidal contractile nanotube in its pre- and postcontraction states.,Ge P, Scholl D, Leiman PG, Yu X, Miller JF, Zhou ZH Nat Struct Mol Biol. 2015 Mar 30. doi~~: ~~10.1038~~/~~nsmb.2995. PMID:25822993<ref>PMID:25822993<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5w5e" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</SX>		</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Egelman~~, E H~~]]	+	[[Category: Pseudomonas aeruginosa]]
-	[[Category: Guerrero-Ferreira~~, R C~~]]	+	[[Category: Egelman EH]]
-	[[Category: Leiman~~, P G~~]]	+	[[Category: Guerrero-Ferreira RC]]
-	[[Category: Taylor~~, N M~~]]	+	[[Category: Leiman PG]]
-	[[Category: Wang, F]]	+	[[Category: Taylor NM]]
-	[[Category: Zheng, W]]	+	[[Category: Wang F]]
-	~~[[Category: Bacteriocin]]~~	+	[[Category: Zheng W]]
-	~~[[Category: Pyocin]]~~	+
-	~~[[Category: Structural protein~~]]	+

OCA at 22:17, 10 April 2020

OCA — Fri, 10 Apr 2020 22:17:30 GMT

←Older revision		Revision as of 22:17, 10 April 2020
Line 3:		Line 3:
	<SX load='5w5e' size='340' side='right' viewer='molstar' caption='[[5w5e]], [[Resolution\|resolution]] 3.50Å' scene=''>		<SX load='5w5e' size='340' side='right' viewer='molstar' caption='[[5w5e]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w5e]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5E OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5W5E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w5e]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5E OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5W5E FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3j9q\|3j9q]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3j9q\|3j9q]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FIIR2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FIIR2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=5w5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w5e OCA], [http://pdbe.org/5w5e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w5e RCSB], [http://www.ebi.ac.uk/pdbsum/5w5e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w5e 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=5w5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w5e OCA], [http://pdbe.org/5w5e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w5e RCSB], [http://www.ebi.ac.uk/pdbsum/5w5e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w5e ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:55, 6 March 2020

OCA — Fri, 06 Mar 2020 19:55:21 GMT

←Older revision		Revision as of 19:55, 6 March 2020
Line 1:		Line 1:

	==Re-refinement of the pyocin tube structure==		==Re-refinement of the pyocin tube structure==
-	<~~StructureSection~~ load='5w5e' size='340' side='right'caption='[[5w5e]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<SX load='5w5e' size='340' side='right' viewer='molstar' caption='[[5w5e]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5w5e]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W5E FirstGlance]. <br>		<table><tr><td colspan='2'>[[5w5e]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W5E FirstGlance]. <br>
Line 20:		Line 20:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Egelman, E H]]		[[Category: Egelman, E H]]

OCA at 09:46, 1 January 2020

OCA — Wed, 01 Jan 2020 09:46:48 GMT

←Older revision		Revision as of 09:46, 1 January 2020
Line 1:		Line 1:

	==Re-refinement of the pyocin tube structure==		==Re-refinement of the pyocin tube structure==
-	<StructureSection load='5w5e' size='340' side='right' caption='[[5w5e]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<StructureSection load='5w5e' size='340' side='right'caption='[[5w5e]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w5e]] is a 30 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W5E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w5e]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W5E FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3j9q\|3j9q]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3j9q\|3j9q]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FIIR2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=5w5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w5e OCA], [http://pdbe.org/5w5e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w5e RCSB], [http://www.ebi.ac.uk/pdbsum/5w5e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w5e ProSAT]</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=5w5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w5e OCA], [http://pdbe.org/5w5e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w5e RCSB], [http://www.ebi.ac.uk/pdbsum/5w5e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w5e ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Egelman, E H]]		[[Category: Egelman, E H]]
	[[Category: Guerrero-Ferreira, R C]]		[[Category: Guerrero-Ferreira, R C]]

OCA: Protected "5w5e" [edit=sysop:move=sysop]

OCA — Thu, 17 Aug 2017 06:05:03 GMT

Protected "5w5e" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:05, 17 August 2017

OCA: New page: ==Re-refinement of the pyocin tube structure== == Structural high...

OCA — Thu, 17 Aug 2017 06:05:01 GMT

New page: ==Re-refinement of the pyocin tube structure== <StructureSection load='5w5e' size='340' side='right' caption='5w5e, resolution 3.50Å' scene=''> == Structural high...

New page

==Re-refinement of the pyocin tube structure==
<StructureSection load='5w5e' size='340' side='right' caption='[[5w5e]], [[Resolution|resolution]] 3.50Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5w5e]] is a 30 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W5E FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3j9q|3j9q]]</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=5w5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w5e OCA], [http://pdbe.org/5w5e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w5e RCSB], [http://www.ebi.ac.uk/pdbsum/5w5e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w5e ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
R-type pyocins are representatives of contractile ejection systems, a class of biological nanomachines that includes, among others, the bacterial type VI secretion system (T6SS) and contractile bacteriophage tails. We report atomic models of the Pseudomonas aeruginosa precontraction pyocin sheath and tube, and the postcontraction sheath, obtained by cryo-EM at 3.5-A and 3.9-A resolutions, respectively. The central channel of the tube is negatively charged, in contrast to the neutral and positive counterparts in T6SSs and phage tails. The sheath is interwoven by long N- and C-terminal extension arms emanating from each subunit, which create an extensive two-dimensional mesh that has the same connectivity in the extended and contracted state of the sheath. We propose that the contraction process draws energy from electrostatic and shape complementarities to insert the inner tube through bacterial cell membranes to eventually kill the bacteria.

Atomic structures of a bactericidal contractile nanotube in its pre- and postcontraction states.,Ge P, Scholl D, Leiman PG, Yu X, Miller JF, Zhou ZH Nat Struct Mol Biol. 2015 Mar 30. doi: 10.1038/nsmb.2995. PMID:25822993<ref>PMID:25822993</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5w5e" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Egelman, E H]]
[[Category: Guerrero-Ferreira, R C]]
[[Category: Leiman, P G]]
[[Category: Taylor, N M]]
[[Category: Wang, F]]
[[Category: Zheng, W]]
[[Category: Bacteriocin]]
[[Category: Pyocin]]
[[Category: Structural protein]]