6yhn - Revision history

OCA at 07:40, 1 May 2024

OCA — Wed, 01 May 2024 07:40:05 GMT

←Older revision		Revision as of 07:40, 1 May 2024
Line 3:		Line 3:
	<StructureSection load='6yhn' size='340' side='right'caption='[[6yhn]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6yhn' size='340' side='right'caption='[[6yhn]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yhn]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_pseudotuberkulosis"_(sic)_pfeiffer_1889 "bacillus pseudotuberkulosis" (sic) pfeiffer 1889~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YHN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YHN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yhn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis Yersinia pseudotuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YHN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YHN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BU3:(R,R)-2,3-BUTANEDIOL'>BU3</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:~~MAGNESIUM+ION~~'>MG</scene>, <scene name='pdbligand=NA:~~SODIUM~~+ION'>NA</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE~~+ION'>~~SO4~~</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]] 1.8Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~CSO~~:~~S-HYDROXYCYSTEINE~~'>~~CSO~~</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BU3:(R,R)-2,3-BUTANEDIOL'>BU3</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cnf ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=633 "Bacillus pseudotuberkulosis" (sic) Pfeiffer 1889])</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=6yhn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yhn OCA], [https://pdbe.org/6yhn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yhn RCSB], [https://www.ebi.ac.uk/pdbsum/6yhn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yhn 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=6yhn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yhn OCA], [~~http~~://pdbe.org/6yhn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6yhn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6yhn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6yhn ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A0N9JNY6_YERPU A0A0N9JNY6_YERPU]
-	Cytotoxic necrotizing factors (CNFs) are bacterial single-chain exotoxins that modulate cytokinetic/oncogenic and inflammatory processes through activation of host cell Rho GTPases. To achieve this, they are secreted, bind surface receptors to induce endocytosis and translocate a catalytic unit into the cytosol to intoxicate host cells. A three-dimensional structure that provides insight into the underlying mechanisms is still lacking. Here, we determined the crystal structure of full-length Yersinia pseudotuberculosis CNFY . CNFY consists of five domains (D1-D5), and by integrating structural and functional data, we demonstrate that D1-3 act as export and translocation module for the catalytic unit (D4-5) and for a fused beta-lactamase reporter protein. We further found that D4, which possesses structural similarity to ADP-ribosyl transferases, but had no equivalent catalytic activity, changed its position to interact extensively with D5 in the crystal structure of the free D4-5 fragment. This liberates D5 from a semi-blocked conformation in full-length CNFY , leading to higher deamidation activity. Finally, we identify CNF translocation modules in several uncharacterized fusion proteins, which suggests their usability as a broad-specificity protein delivery tool.	+
-		+
-	Crystal structure of bacterial cytotoxic necrotizing factor CNFY reveals molecular building blocks for intoxication.,Chaoprasid P, Lukat P, Muhlen S, Heidler T, Gazdag EM, Dong S, Bi W, Ruter C, Kirchenwitz M, Steffen A, Jansch L, Stradal TEB, Dersch P, Blankenfeldt W EMBO J. 2021 Jan 7:~~e105202. doi: 10.15252~~/~~embj.2020105202. PMID:33410511<ref>PMID:33410511<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6yhn" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Blankenfeldt, W~~]]	+	[[Category: Yersinia pseudotuberculosis]]
-	[[Category: ~~Gazdag, E M~~]]	+	[[Category: Blankenfeldt W]]
-	[[Category: ~~Heidler, T V~~]]	+	[[Category: Gazdag EM]]
-	[[Category: ~~Lukat, P~~]]	+	[[Category: Heidler TV]]
-	[[Category: ~~Cnf]]~~	+	[[Category: Lukat P]]
-	~~[[Category: Cytotoxic necrotizing factor]]~~	+
-	~~[[Category: Deamidase]]~~	+
-	~~[[Category: Putative adp-ribosyltransferase]]~~	+
-	~~[[Category: Rhoa activation]]~~	+
-	~~[[Category: Rhoa modification]]~~	+
-	~~[[Category: Toxin~~]]	+

OCA at 08:24, 20 January 2021

OCA — Wed, 20 Jan 2021 08:24:41 GMT

←Older revision		Revision as of 08:24, 20 January 2021
Line 1:		Line 1:

	==Crystal structure of domains 4-5 of CNFy from Yersinia pseudotuberculosis==		==Crystal structure of domains 4-5 of CNFy from Yersinia pseudotuberculosis==
-	<StructureSection load='6yhn' size='340' side='right'caption='[[6yhn]]' scene=''>	+	<StructureSection load='6yhn' size='340' side='right'caption='[[6yhn]], [[Resolution\|resolution]] 1.80Å' 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=6YHN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YHN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yhn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pseudotuberkulosis"_(sic)_pfeiffer_1889 "bacillus pseudotuberkulosis" (sic) pfeiffer 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YHN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YHN 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=6yhn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yhn OCA], [http://pdbe.org/6yhn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yhn RCSB], [http://www.ebi.ac.uk/pdbsum/6yhn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yhn ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BU3:(R,R)-2,3-BUTANEDIOL'>BU3</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cnf ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=633 "Bacillus pseudotuberkulosis" (sic) Pfeiffer 1889])</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=6yhn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yhn OCA], [http://pdbe.org/6yhn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yhn RCSB], [http://www.ebi.ac.uk/pdbsum/6yhn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yhn ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cytotoxic necrotizing factors (CNFs) are bacterial single-chain exotoxins that modulate cytokinetic/oncogenic and inflammatory processes through activation of host cell Rho GTPases. To achieve this, they are secreted, bind surface receptors to induce endocytosis and translocate a catalytic unit into the cytosol to intoxicate host cells. A three-dimensional structure that provides insight into the underlying mechanisms is still lacking. Here, we determined the crystal structure of full-length Yersinia pseudotuberculosis CNFY . CNFY consists of five domains (D1-D5), and by integrating structural and functional data, we demonstrate that D1-3 act as export and translocation module for the catalytic unit (D4-5) and for a fused beta-lactamase reporter protein. We further found that D4, which possesses structural similarity to ADP-ribosyl transferases, but had no equivalent catalytic activity, changed its position to interact extensively with D5 in the crystal structure of the free D4-5 fragment. This liberates D5 from a semi-blocked conformation in full-length CNFY , leading to higher deamidation activity. Finally, we identify CNF translocation modules in several uncharacterized fusion proteins, which suggests their usability as a broad-specificity protein delivery tool.
		+
		+	Crystal structure of bacterial cytotoxic necrotizing factor CNFY reveals molecular building blocks for intoxication.,Chaoprasid P, Lukat P, Muhlen S, Heidler T, Gazdag EM, Dong S, Bi W, Ruter C, Kirchenwitz M, Steffen A, Jansch L, Stradal TEB, Dersch P, Blankenfeldt W EMBO J. 2021 Jan 7:e105202. doi: 10.15252/embj.2020105202. PMID:33410511<ref>PMID:33410511</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yhn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Blankenfeldt W]]	+	[[Category: Blankenfeldt, W]]
-	[[Category: Gazdag EM]]	+	[[Category: Gazdag, E M]]
-	[[Category: Heidler TV]]	+	[[Category: Heidler, T V]]
-	[[Category: Lukat P]]	+	[[Category: Lukat, P]]
		+	[[Category: Cnf]]
		+	[[Category: Cytotoxic necrotizing factor]]
		+	[[Category: Deamidase]]
		+	[[Category: Putative adp-ribosyltransferase]]
		+	[[Category: Rhoa activation]]
		+	[[Category: Rhoa modification]]
		+	[[Category: Toxin]]

OCA at 06:45, 30 December 2020

OCA — Wed, 30 Dec 2020 06:45:19 GMT

←Older revision		Revision as of 06:45, 30 December 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6yhn is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of domains 4-5 of CNFy from Yersinia pseudotuberculosis==
-		+	<StructureSection load='6yhn' size='340' side='right'caption='[[6yhn]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YHN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YHN FirstGlance]. <br>
-	~~Description~~:	+	</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=6yhn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yhn OCA], [http://pdbe.org/6yhn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yhn RCSB], [http://www.ebi.ac.uk/pdbsum/6yhn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yhn ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Blankenfeldt W]]
		+	[[Category: Gazdag EM]]
		+	[[Category: Heidler TV]]
		+	[[Category: Lukat P]]

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

OCA — Wed, 08 Apr 2020 05:43:54 GMT

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

←Older revision

Revision as of 05:43, 8 April 2020

OCA: New page: '''Unreleased structure''' The entry 6yhn is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 08 Apr 2020 05:43:53 GMT

New page: '''Unreleased structure''' The entry 6yhn is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6yhn is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]