6ar6 - Revision history

OCA at 14:18, 13 March 2024

OCA — Wed, 13 Mar 2024 14:18:03 GMT

←Older revision		Revision as of 14:18, 13 March 2024
Line 3:		Line 3:
	<SX load='6ar6' size='340' side='right' viewer='molstar' caption='[[6ar6]], [[Resolution\|resolution]] 9.00Å' scene=''>		<SX load='6ar6' size='340' side='right' viewer='molstar' caption='[[6ar6]], [[Resolution\|resolution]] 9.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ar6]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935~~] and [~~http~~://en.wikipedia.org/wiki/~~Drome Drome~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AR6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6AR6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ar6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridioides_difficile Clostridioides difficile] and [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AR6 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>toxB, tcdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1496~~ "~~Bacillus difficilis~~" ~~Hall and O'Toole 1935~~])</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]] 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=6ar6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ar6 OCA], [~~http~~://pdbe.org/6ar6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ar6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ar6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ar6 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=6ar6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ar6 OCA], [https://pdbe.org/6ar6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ar6 RCSB], [https://www.ebi.ac.uk/pdbsum/6ar6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ar6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~TOXB_CLODI TOXB_CLODI~~]] ~~Cytotoxin~~.	+	[https://www.uniprot.org/uniprot/TCDB_CLODI TCDB_CLODI] Precursor of a cytotoxin that targets and disrupts the colonic epithelium, inducing the host inflammatory and innate immune responses and resulting in diarrhea and pseudomembranous colitis (PubMed:20844489, PubMed:24919149). TcdB constitutes the main toxin that mediates the pathology of C.difficile infection, an opportunistic pathogen that colonizes the colon when the normal gut microbiome is disrupted (PubMed:19252482, PubMed:20844489). Compared to TcdA, TcdB is more virulent and more important for inducing the host inflammatory and innate immune responses (PubMed:19252482, PubMed:24919149). This form constitutes the precursor of the toxin: it enters into host cells and mediates autoprocessing to release the active toxin (Glucosyltransferase TcdB) into the host cytosol (PubMed:10768933, PubMed:11152463, PubMed:12941936, PubMed:17334356, PubMed:20498856). Targets colonic epithelia by binding to the frizzled receptors FZD1, FZD2 and FZD7, and enters host cells via clathrin-mediated endocytosis (PubMed:27680706). Frizzled receptors constitute the major host receptors in the colonic epithelium, but other receptors, such as CSPG4 or NECTIN3/PVRL3, have been identified (PubMed:25547119, PubMed:26038560, PubMed:27680706). Binding to carbohydrates and sulfated glycosaminoglycans on host cell surface also contribute to entry into cells (By similarity). Once entered into host cells, acidification in the endosome promotes the membrane insertion of the translocation region and formation of a pore, leading to translocation of the GT44 and peptidase C80 domains across the endosomal membrane (PubMed:11152463, PubMed:12941936, PubMed:24567384). This activates the peptidase C80 domain and autocatalytic processing, releasing the N-terminal part (Glucosyltransferase TcdB), which constitutes the active part of the toxin, in the cytosol (PubMed:17334356, PubMed:27571750).[UniProtKB:P16154]<ref>PMID:10768933</ref> <ref>PMID:11152463</ref> <ref>PMID:12941936</ref> <ref>PMID:17334356</ref> <ref>PMID:19252482</ref> <ref>PMID:20498856</ref> <ref>PMID:20844489</ref> <ref>PMID:24567384</ref> <ref>PMID:24919149</ref> <ref>PMID:25547119</ref> <ref>PMID:26038560</ref> <ref>PMID:27571750</ref> <ref>PMID:27680706</ref> Active form of the toxin, which is released into the host cytosol following autoprocessing and inactivates small GTPases (PubMed:8144660, PubMed:7777059, PubMed:16157585, PubMed:17901056, PubMed:24905543, PubMed:24919149). Acts by mediating monoglucosylation of small GTPases of the Rho family (Rac1, RhoA, RhoB, RhoC, RhoG and Cdc42) in host cells at the conserved threonine residue located in the switch I region ('Thr-37/35'), using UDP-alpha-D-glucose as the sugar donor (PubMed:7777059, PubMed:16157585, PubMed:17901056, PubMed:24905543, PubMed:24919149). Monoglucosylation of host small GTPases completely prevents the recognition of the downstream effector, blocking the GTPases in their inactive form, leading to actin cytoskeleton disruption and cell death, resulting in the loss of colonic epithelial barrier function (PubMed:7777059, PubMed:24919149).<ref>PMID:16157585</ref> <ref>PMID:17901056</ref> <ref>PMID:24905543</ref> <ref>PMID:24919149</ref> <ref>PMID:7777059</ref> <ref>PMID:8144660</ref>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: ~~Bacillus difficilis hall and o'toole 1935~~]]	+	[[Category: Clostridioides difficile]]
-	[[Category: ~~Drome~~]]	+	[[Category: Drosophila melanogaster]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jiang, M]]	+	[[Category: Jiang M]]
-	[[Category: Zhang, J]]	+	[[Category: Zhang J]]
-	~~[[Category: Toxin-protein binding complex~~]]	+

OCA at 23:08, 10 April 2020

OCA — Fri, 10 Apr 2020 23:08:47 GMT

←Older revision		Revision as of 23:08, 10 April 2020
Line 3:		Line 3:
	<SX load='6ar6' size='340' side='right' viewer='molstar' caption='[[6ar6]], [[Resolution\|resolution]] 9.00Å' scene=''>		<SX load='6ar6' size='340' side='right' viewer='molstar' caption='[[6ar6]], [[Resolution\|resolution]] 9.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ar6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935] and [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AR6 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6AR6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ar6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935] and [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AR6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6AR6 FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">toxB, tcdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1496 "Bacillus difficilis" Hall and O'Toole 1935])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">toxB, tcdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1496 "Bacillus difficilis" Hall and O'Toole 1935])</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=6ar6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ar6 OCA], [http://pdbe.org/6ar6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ar6 RCSB], [http://www.ebi.ac.uk/pdbsum/6ar6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ar6 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=6ar6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ar6 OCA], [http://pdbe.org/6ar6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ar6 RCSB], [http://www.ebi.ac.uk/pdbsum/6ar6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ar6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 20:25, 6 March 2020

OCA — Fri, 06 Mar 2020 20:25:21 GMT

←Older revision		Revision as of 20:25, 6 March 2020
Line 1:		Line 1:

	==Clostridioides difficile toxinB with DLD-4 darpin==		==Clostridioides difficile toxinB with DLD-4 darpin==
-	<~~StructureSection~~ load='6ar6' size='340' side='right'caption='[[6ar6]], [[Resolution\|resolution]] 9.00Å' scene=''>	+	<SX load='6ar6' size='340' side='right' viewer='molstar' caption='[[6ar6]], [[Resolution\|resolution]] 9.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ar6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935] and [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AR6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AR6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ar6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935] and [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AR6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AR6 FirstGlance]. <br>
Line 10:		Line 10:
	[[http://www.uniprot.org/uniprot/TOXB_CLODI TOXB_CLODI]] Cytotoxin.		[[http://www.uniprot.org/uniprot/TOXB_CLODI TOXB_CLODI]] Cytotoxin.
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Bacillus difficilis hall and o'toole 1935]]		[[Category: Bacillus difficilis hall and o'toole 1935]]
	[[Category: Drome]]		[[Category: Drome]]

OCA at 10:05, 1 January 2020

OCA — Wed, 01 Jan 2020 10:05:02 GMT

←Older revision		Revision as of 10:05, 1 January 2020
Line 1:		Line 1:

	==Clostridioides difficile toxinB with DLD-4 darpin==		==Clostridioides difficile toxinB with DLD-4 darpin==
-	<StructureSection load='6ar6' size='340' side='right' caption='[[6ar6]], [[Resolution\|resolution]] 9.00Å' scene=''>	+	<StructureSection load='6ar6' size='340' side='right'caption='[[6ar6]], [[Resolution\|resolution]] 9.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ar6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935] and [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AR6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AR6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ar6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935] and [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AR6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AR6 FirstGlance]. <br>
Line 13:		Line 13:
	[[Category: Bacillus difficilis hall and o'toole 1935]]		[[Category: Bacillus difficilis hall and o'toole 1935]]
	[[Category: Drome]]		[[Category: Drome]]
		+	[[Category: Large Structures]]
	[[Category: Jiang, M]]		[[Category: Jiang, M]]
	[[Category: Zhang, J]]		[[Category: Zhang, J]]
	[[Category: Toxin-protein binding complex]]		[[Category: Toxin-protein binding complex]]

OCA at 07:42, 21 February 2019

OCA — Thu, 21 Feb 2019 07:42:38 GMT

←Older revision		Revision as of 07:42, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='6ar6' size='340' side='right' caption='[[6ar6]], [[Resolution\|resolution]] 9.00Å' scene=''>		<StructureSection load='6ar6' size='340' side='right' caption='[[6ar6]], [[Resolution\|resolution]] 9.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ar6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AR6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AR6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ar6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935] and [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AR6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AR6 FirstGlance]. <br>
-	</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=6ar6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ar6 OCA], [http://pdbe.org/6ar6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ar6 RCSB], [http://www.ebi.ac.uk/pdbsum/6ar6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ar6 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">toxB, tcdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1496 "Bacillus difficilis" Hall and O'Toole 1935])</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=6ar6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ar6 OCA], [http://pdbe.org/6ar6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ar6 RCSB], [http://www.ebi.ac.uk/pdbsum/6ar6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ar6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 10:		Line 11:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus difficilis hall and o'toole 1935]]
		+	[[Category: Drome]]
	[[Category: Jiang, M]]		[[Category: Jiang, M]]
	[[Category: Zhang, J]]		[[Category: Zhang, J]]
	[[Category: Toxin-protein binding complex]]		[[Category: Toxin-protein binding complex]]

OCA at 06:03, 22 August 2018

OCA — Wed, 22 Aug 2018 06:03:47 GMT

←Older revision		Revision as of 06:03, 22 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ar6 ~~is ON HOLD until Paper Publication~~	+	==Clostridioides difficile toxinB with DLD-4 darpin==
-		+	<StructureSection load='6ar6' size='340' side='right' caption='[[6ar6]], [[Resolution\|resolution]] 9.00Å' scene=''>
-	~~Authors~~: ~~Zhang~~, J., ~~Jiang~~, M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ar6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AR6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AR6 FirstGlance]. <br>
-	~~Description~~: ~~Clostridioides difficile toxinB with DLD~~-~~4 darpin~~	+	</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=6ar6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ar6 OCA], [http://pdbe.org/6ar6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ar6 RCSB], [http://www.ebi.ac.uk/pdbsum/6ar6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ar6 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TOXB_CLODI TOXB_CLODI]] Cytotoxin.
		+	__TOC__
		+	</StructureSection>
	[[Category: Jiang, M]]		[[Category: Jiang, M]]
	[[Category: Zhang, J]]		[[Category: Zhang, J]]
		+	[[Category: Toxin-protein binding complex]]

OCA: Protected "6ar6" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:41:56 GMT

Protected "6ar6" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:41, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 6ar6 is ON HOLD until Paper Publication Authors: Zhang, J., Jiang, M. Description: Clostridioides difficile toxinB with DLD-4 darpin [[Category: Un...

OCA — Wed, 27 Sep 2017 16:41:55 GMT

New page: '''Unreleased structure''' The entry 6ar6 is ON HOLD until Paper Publication Authors: Zhang, J., Jiang, M. Description: Clostridioides difficile toxinB with DLD-4 darpin [[Category: Un...

New page

'''Unreleased structure'''

The entry 6ar6 is ON HOLD until Paper Publication

Authors: Zhang, J., Jiang, M.

Description: Clostridioides difficile toxinB with DLD-4 darpin
[[Category: Unreleased Structures]]
[[Category: Jiang, M]]
[[Category: Zhang, J]]