6klx - Revision history

OCA at 10:43, 27 March 2024

OCA — Wed, 27 Mar 2024 10:43:20 GMT

←Older revision		Revision as of 10:43, 27 March 2024
Line 3:		Line 3:
	<SX load='6klx' size='340' side='right' viewer='molstar' caption='[[6klx]], [[Resolution\|resolution]] 2.90Å' scene=''>		<SX load='6klx' size='340' side='right' viewer='molstar' caption='[[6klx]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6klx]] is a 7 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus~~ perfringens~~" veillon and zuber 1898~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KLX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6KLX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6klx]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KLX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KLX FirstGlance]. <br>
-	</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></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]] 2.9Å</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=6klx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6klx OCA], [~~http~~://pdbe.org/6klx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6klx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6klx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6klx ProSAT]</span></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></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=6klx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6klx OCA], [https://pdbe.org/6klx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6klx RCSB], [https://www.ebi.ac.uk/pdbsum/6klx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6klx ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q46221_CLOPF Q46221_CLOPF]
-	~~The iota toxin produced by Clostridium perfringens type E is a binary toxin comprising two independent polypeptides~~: Ia, an ADP-ribosyltransferase, and Ib, which is involved in cell binding and translocation of Ia across the cell membrane. Here we report cryo-EM structures of the translocation channel Ib-pore and its complex with Ia. The high-resolution Ib-pore structure demonstrates a similar structural framework to that of the catalytic varphi-clamp of the anthrax protective antigen pore. However, the Ia-bound Ib-pore structure shows a unique binding mode of Ia: one Ia binds to the Ib-pore, and the Ia amino-terminal domain forms multiple weak interactions with two additional Ib-pore constriction sites. Furthermore, Ib-binding induces tilting and partial unfolding of the Ia N-terminal alpha-helix, permitting its extension to the varphi-clamp gate. This new mechanism of N-terminal unfolding is crucial for protein translocation.	+
-		+
-	Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex.,Yamada T, Yoshida T, Kawamoto A, Mitsuoka K, Iwasaki K, Tsuge H Nat Struct Mol Biol. 2020 Mar;27(3):288-296. doi: 10.1038/~~s41594-020-0388-6. Epub, 2020 Mar 2. PMID:32123390<ref>PMID:32123390<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6klx" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: ~~Bacillus~~ perfringens ~~veillon and zuber 1898~~]]	+	[[Category: Clostridium perfringens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Iwasaki, K]]	+	[[Category: Iwasaki K]]
-	[[Category: Kawamoto, A]]	+	[[Category: Kawamoto A]]
-	[[Category: Mitsuoka, K]]	+	[[Category: Mitsuoka K]]
-	[[Category: Tsuge, H]]	+	[[Category: Tsuge H]]
-	[[Category: Yamada, T]]	+	[[Category: Yamada T]]
-	[[Category: Yoshida, T]]	+	[[Category: Yoshida T]]
-	~~[[Category: Adp-ribosylation]]~~	+
-	~~[[Category: Bacterial binary toxin]]~~	+
-	~~[[Category: Protein translocation channel]]~~	+
-	~~[[Category: Toxin~~]]	+

OCA at 02:28, 11 April 2020

OCA — Sat, 11 Apr 2020 02:28:23 GMT

←Older revision		Revision as of 02:28, 11 April 2020
Line 3:		Line 3:
	<SX load='6klx' size='340' side='right' viewer='molstar' caption='[[6klx]], [[Resolution\|resolution]] 2.90Å' scene=''>		<SX load='6klx' size='340' side='right' viewer='molstar' caption='[[6klx]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6klx]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KLX OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KLX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6klx]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KLX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KLX 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></td></tr>	+	</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></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=6klx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6klx OCA], [http://pdbe.org/6klx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6klx RCSB], [http://www.ebi.ac.uk/pdbsum/6klx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6klx 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=6klx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6klx OCA], [http://pdbe.org/6klx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6klx RCSB], [http://www.ebi.ac.uk/pdbsum/6klx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6klx ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:14, 18 March 2020

OCA — Wed, 18 Mar 2020 10:14:55 GMT

←Older revision		Revision as of 10:14, 18 March 2020
Line 7:		Line 7:
	<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=6klx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6klx OCA], [http://pdbe.org/6klx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6klx RCSB], [http://www.ebi.ac.uk/pdbsum/6klx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6klx 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=6klx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6klx OCA], [http://pdbe.org/6klx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6klx RCSB], [http://www.ebi.ac.uk/pdbsum/6klx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6klx ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The iota toxin produced by Clostridium perfringens type E is a binary toxin comprising two independent polypeptides: Ia, an ADP-ribosyltransferase, and Ib, which is involved in cell binding and translocation of Ia across the cell membrane. Here we report cryo-EM structures of the translocation channel Ib-pore and its complex with Ia. The high-resolution Ib-pore structure demonstrates a similar structural framework to that of the catalytic varphi-clamp of the anthrax protective antigen pore. However, the Ia-bound Ib-pore structure shows a unique binding mode of Ia: one Ia binds to the Ib-pore, and the Ia amino-terminal domain forms multiple weak interactions with two additional Ib-pore constriction sites. Furthermore, Ib-binding induces tilting and partial unfolding of the Ia N-terminal alpha-helix, permitting its extension to the varphi-clamp gate. This new mechanism of N-terminal unfolding is crucial for protein translocation.
		+
		+	Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex.,Yamada T, Yoshida T, Kawamoto A, Mitsuoka K, Iwasaki K, Tsuge H Nat Struct Mol Biol. 2020 Mar;27(3):288-296. doi: 10.1038/s41594-020-0388-6. Epub, 2020 Mar 2. PMID:32123390<ref>PMID:32123390</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6klx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</SX>		</SX>

OCA at 22:26, 6 March 2020

OCA — Fri, 06 Mar 2020 22:26:43 GMT

←Older revision		Revision as of 22:26, 6 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6klx is ~~ON HOLD until Paper Publication~~	+	==Pore structure of Iota toxin binding component (Ib)==
-		+	<SX load='6klx' size='340' side='right' viewer='molstar' caption='[[6klx]], [[Resolution\|resolution]] 2.90Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6klx]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KLX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KLX FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=6klx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6klx OCA], [http://pdbe.org/6klx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6klx RCSB], [http://www.ebi.ac.uk/pdbsum/6klx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6klx ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</SX>
		+	[[Category: Bacillus perfringens veillon and zuber 1898]]
		+	[[Category: Large Structures]]
		+	[[Category: Iwasaki, K]]
		+	[[Category: Kawamoto, A]]
		+	[[Category: Mitsuoka, K]]
		+	[[Category: Tsuge, H]]
		+	[[Category: Yamada, T]]
		+	[[Category: Yoshida, T]]
		+	[[Category: Adp-ribosylation]]
		+	[[Category: Bacterial binary toxin]]
		+	[[Category: Protein translocation channel]]
		+	[[Category: Toxin]]

OCA at 14:54, 14 August 2019

OCA — Wed, 14 Aug 2019 14:54:38 GMT

←Older revision		Revision as of 14:54, 14 August 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6klx is ON HOLD	+	The entry 6klx is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 07 Aug 2019 04:10:22 GMT

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

←Older revision

Revision as of 04:10, 7 August 2019

OCA: New page: '''Unreleased structure''' The entry 6klx is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 07 Aug 2019 04:10:21 GMT

New page: '''Unreleased structure''' The entry 6klx is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6klx is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]