6cl6 - Revision history

OCA at 14:28, 13 March 2024

OCA — Wed, 13 Mar 2024 14:28:58 GMT

←Older revision		Revision as of 14:28, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6cl6' size='340' side='right'caption='[[6cl6]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6cl6' size='340' side='right'caption='[[6cl6]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cl6]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CL6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CL6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cl6]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CL6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CL6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.898Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA0620 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=6cl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cl6 OCA], [~~http~~://pdbe.org/6cl6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6cl6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6cl6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6cl6 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=6cl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cl6 OCA], [https://pdbe.org/6cl6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cl6 RCSB], [https://www.ebi.ac.uk/pdbsum/6cl6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cl6 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/G3XD71_PSEAE G3XD71_PSEAE]
-	The R-type pyocins are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. Structurally, the R-type pyocins are similar to "simple" contractile tails, such as those of phage P2 and Mu. The pyocin recognizes and binds to its target with the help of fibers that emanate from the baseplate structure at one end of the particle. Subsequently, the pyocin contracts its sheath and drives the rigid tube through the host cell envelope. This causes depolarization of the cytoplasmic membrane and cell death. The host cell surface-binding fiber is ~340 A-long and is attached to the baseplate with its N-terminal domain. Here, we report the crystal structures of C-terminal fragments of the R1 and R2 pyocin fibers that comprise the distal, receptor-binding part of the protein. Both proteins are ~240 A-long homotrimers in which slender rod-like domains are interspersed with more globular domains-two tandem knob domains in the N-terminal part of the fragment and a lectin-like domain at its C-terminus. The putative substrate binding sites are separated by about 100 A, suggesting that binding of the fiber to the cell surface causes the fiber to adopt a certain orientation relative to the baseplate and this then triggers sheath contraction.	+
-		+
-	~~Structure and Analysis of R1 and R2 Pyocin Receptor-Binding Fibers.,Buth SA, Shneider MM, Scholl D, Leiman PG Viruses. 2018 Aug 14;10(8). pii~~: ~~v10080427. doi: 10.3390~~/~~v10080427. PMID:30110933<ref>PMID:30110933<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6cl6" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseae~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Buth~~, S A~~]]	+	[[Category: Buth SA]]
-	[[Category: Leiman~~, P G~~]]	+	[[Category: Leiman PG]]
-	[[Category: Shneider~~, M M]]~~	+	[[Category: Shneider MM]]
-	~~[[Category: Contractile injection system]]~~	+
-	~~[[Category: Pseudomonas aeruginosa]]~~	+
-	~~[[Category: R-type pyocin]]~~	+
-	~~[[Category: Receptor-binding protein]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 12:29, 17 July 2019

OCA — Wed, 17 Jul 2019 12:29:06 GMT

←Older revision		Revision as of 12:29, 17 July 2019
Line 1:		Line 1:

	==Structure of P. aeruginosa R2 pyocin fiber PA0620 comprising C-terminal residues 323-691==		==Structure of P. aeruginosa R2 pyocin fiber PA0620 comprising C-terminal residues 323-691==
-	<StructureSection load='6cl6' size='340' side='right' caption='[[6cl6]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='6cl6' size='340' side='right'caption='[[6cl6]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cl6]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CL6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CL6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cl6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CL6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CL6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA0620 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=6cl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cl6 OCA], [http://pdbe.org/6cl6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cl6 RCSB], [http://www.ebi.ac.uk/pdbsum/6cl6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cl6 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=6cl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cl6 OCA], [http://pdbe.org/6cl6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cl6 RCSB], [http://www.ebi.ac.uk/pdbsum/6cl6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cl6 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The R-type pyocins are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. Structurally, the R-type pyocins are similar to "simple" contractile tails, such as those of phage P2 and Mu. The pyocin recognizes and binds to its target with the help of fibers that emanate from the baseplate structure at one end of the particle. Subsequently, the pyocin contracts its sheath and drives the rigid tube through the host cell envelope. This causes depolarization of the cytoplasmic membrane and cell death. The host cell surface-binding fiber is ~340 A-long and is attached to the baseplate with its N-terminal domain. Here, we report the crystal structures of C-terminal fragments of the R1 and R2 pyocin fibers that comprise the distal, receptor-binding part of the protein. Both proteins are ~240 A-long homotrimers in which slender rod-like domains are interspersed with more globular domains-two tandem knob domains in the N-terminal part of the fragment and a lectin-like domain at its C-terminus. The putative substrate binding sites are separated by about 100 A, suggesting that binding of the fiber to the cell surface causes the fiber to adopt a certain orientation relative to the baseplate and this then triggers sheath contraction.
		+
		+	Structure and Analysis of R1 and R2 Pyocin Receptor-Binding Fibers.,Buth SA, Shneider MM, Scholl D, Leiman PG Viruses. 2018 Aug 14;10(8). pii: v10080427. doi: 10.3390/v10080427. PMID:30110933<ref>PMID:30110933</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6cl6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pseae]]
	[[Category: Buth, S A]]		[[Category: Buth, S A]]
	[[Category: Leiman, P G]]		[[Category: Leiman, P G]]

OCA at 05:36, 27 June 2018

OCA — Wed, 27 Jun 2018 05:36:16 GMT

←Older revision		Revision as of 05:36, 27 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6cl6 is ON HOLD until Jun 27 2019~~	+	==Structure of P. aeruginosa R2 pyocin fiber PA0620 comprising C-terminal residues 323-691==
-		+	<StructureSection load='6cl6' size='340' side='right' caption='[[6cl6]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~Authors: Buth, S.A., Shneider, M.M., Leiman, P.G.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6cl6]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CL6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CL6 FirstGlance]. <br>
-	~~Description:~~ Structure of P. aeruginosa R2 pyocin fiber PA0620 comprising C-terminal residues 323-691 (~~CASP target~~)	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6cl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cl6 OCA], [http://pdbe.org/6cl6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cl6 RCSB], [http://www.ebi.ac.uk/pdbsum/6cl6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cl6 ProSAT]</span></td></tr>
-	[[Category: Leiman, P.G]]	+	</table>
-	[[Category: Shneider, M.M]]	+	__TOC__
-	[[Category: ~~Buth, S.A~~]]	+	</StructureSection>
		+	[[Category: Buth, S A]]
		+	[[Category: Leiman, P G]]
		+	[[Category: Shneider, M M]]
		+	[[Category: Contractile injection system]]
		+	[[Category: Pseudomonas aeruginosa]]
		+	[[Category: R-type pyocin]]
		+	[[Category: Receptor-binding protein]]
		+	[[Category: Viral protein]]

OCA at 06:37, 2 May 2018

OCA — Wed, 02 May 2018 06:37:57 GMT

←Older revision		Revision as of 06:37, 2 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6cl6 is ON HOLD	+	The entry 6cl6 is ON HOLD until Jun 27 2019

	Authors: Buth, S.A., Shneider, M.M., Leiman, P.G.		Authors: Buth, S.A., Shneider, M.M., Leiman, P.G.

OCA at 04:38, 4 April 2018

OCA — Wed, 04 Apr 2018 04:38:11 GMT

←Older revision		Revision as of 04:38, 4 April 2018
Line 5:		Line 5:
	Authors: Buth, S.A., Shneider, M.M., Leiman, P.G.		Authors: Buth, S.A., Shneider, M.M., Leiman, P.G.

-	Description: Structure of P. aeruginosa R2 pyocin fiber PA0620 comprising C-terminal residues 323-691	+	Description: Structure of P. aeruginosa R2 pyocin fiber PA0620 comprising C-terminal residues 323-691 (CASP target)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Buth, S.A]]
	[[Category: Leiman, P.G]]		[[Category: Leiman, P.G]]
	[[Category: Shneider, M.M]]		[[Category: Shneider, M.M]]
		+	[[Category: Buth, S.A]]

OCA: Protected "6cl6" [edit=sysop:move=sysop]

OCA — Thu, 08 Mar 2018 03:52:47 GMT

Protected "6cl6" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:52, 8 March 2018

OCA: New page: '''Unreleased structure''' The entry 6cl6 is ON HOLD Authors: Buth, S.A., Shneider, M.M., Leiman, P.G. Description: Structure of P. aeruginosa R2 pyocin fiber PA0620 comprising C-termi...

OCA — Thu, 08 Mar 2018 03:52:45 GMT

New page: '''Unreleased structure''' The entry 6cl6 is ON HOLD Authors: Buth, S.A., Shneider, M.M., Leiman, P.G. Description: Structure of P. aeruginosa R2 pyocin fiber PA0620 comprising C-termi...

New page

'''Unreleased structure'''

The entry 6cl6 is ON HOLD

Authors: Buth, S.A., Shneider, M.M., Leiman, P.G.

Description: Structure of P. aeruginosa R2 pyocin fiber PA0620 comprising C-terminal residues 323-691
[[Category: Unreleased Structures]]
[[Category: Buth, S.A]]
[[Category: Leiman, P.G]]
[[Category: Shneider, M.M]]