5ybi - Revision history

OCA at 08:25, 22 November 2023

OCA — Wed, 22 Nov 2023 08:25:59 GMT

←Older revision		Revision as of 08:25, 22 November 2023
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	<StructureSection load='5ybi' size='340' side='right'caption='[[5ybi]], [[Resolution\|resolution]] 2.27Å' scene=''>		<StructureSection load='5ybi' size='340' side='right'caption='[[5ybi]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ybi]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YBI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ybi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YBI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID~~-~~ADENYLATE+ESTER'>ANP</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.268Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[2obm\|2obm]]~~, ~~[[5ybh\|5ybh]]~~<~~/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=5ybi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybi OCA], [https://pdbe.org/5ybi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ybi RCSB], [https://www.ebi.ac.uk/pdbsum/5ybi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybi ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">spaL~~, ~~mxiB, spa47, CP0149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 "Shigella paradysenteriae" Weldin 1927])~~<~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/H(+)-transporting_two-sector_ATPase H(+)-transporting two-sector ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.14 3.6.3.14]~~ </~~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=5ybi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybi OCA], [~~http~~://pdbe.org/5ybi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ybi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ybi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybi ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~SPAL_SHIFL SPAL_SHIFL~~]~~] Required for surface presentation~~ of ~~invasion plasmid antigens~~. ~~Probable catalytic subunit of~~ a ~~protein translocase~~. Required for invasion and ~~for secretion~~ of the ~~three IPA proteins~~.	+	[https://www.uniprot.org/uniprot/SCTN_SHIFL SCTN_SHIFL] ATPase component of the type III secretion system (T3SS), also called injectisome, which is used to inject bacterial effector proteins into eukaryotic host cells (PubMed:26947936, PubMed:27770024, PubMed:29595954). Acts as a molecular motor to provide the energy that is required for the export of proteins (Probable). Required for type III secretion apparatus (T3SA) formation, proper protein secretion, host cell invasion and virulence (PubMed:26947936, PubMed:27770024, PubMed:31162724). May play a critical role in T3SS substrate recognition, disassembly of the effector/chaperone complex and unfolding of the effector in an ATP-dependent manner prior to secretion (By similarity).[UniProtKB:P0A1B9]<ref>PMID:26947936</ref> <ref>PMID:27770024</ref> <ref>PMID:29595954</ref> <ref>PMID:31162724</ref> <ref>PMID:26947936</ref> <ref>PMID:27770024</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Shigella paradysenteriae weldin 1927]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Cui, S~~]]	+	[[Category: Shigella flexneri]]
-	[[Category: ~~Gao, X P~~]]	+	[[Category: Cui S]]
-	[[Category: ~~Mu, Z X~~]]	+	[[Category: Gao XP]]
-	[[Category: ~~Amppnp]]~~	+	[[Category: Mu ZX]]
-	~~[[Category: Atpase]]~~	+
-	~~[[Category: Hexamer]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: T3ss~~]]	+

OCA at 09:14, 18 December 2019

OCA — Wed, 18 Dec 2019 09:14:10 GMT

←Older revision		Revision as of 09:14, 18 December 2019
Line 1:		Line 1:

	==Structure of the bacterial pathogens ATPase with substrate AMPPNP==		==Structure of the bacterial pathogens ATPase with substrate AMPPNP==
-	<StructureSection load='5ybi' size='340' side='right' caption='[[5ybi]], [[Resolution\|resolution]] 2.27Å' scene=''>	+	<StructureSection load='5ybi' size='340' side='right'caption='[[5ybi]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ybi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YBI FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ybi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YBI FirstGlance]. <br>
Line 13:		Line 13:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SPAL_SHIFL SPAL_SHIFL]] Required for surface presentation of invasion plasmid antigens. Probable catalytic subunit of a protein translocase. Required for invasion and for secretion of the three IPA proteins.		[[http://www.uniprot.org/uniprot/SPAL_SHIFL SPAL_SHIFL]] Required for surface presentation of invasion plasmid antigens. Probable catalytic subunit of a protein translocase. Required for invasion and for secretion of the three IPA proteins.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Gram-negative bacteria utilize the type III secretion system (T3SS) to inject effector proteins into the host cell cytoplasm, where they subvert cellular functions and assist pathogen invasion. The conserved type III-associated ATPase is critical for the separation of chaperones from effector proteins, the unfolding of effector proteins and translocating them through the narrow channel of the secretion apparatus. However, how ATP hydrolysis is coupled to the mechanical work of the enzyme remains elusive. Herein, we present a complete description of nucleoside triphosphate binding by surface presentation antigens 47 (Spa47) from Shigella flexneri, based on crystal structures containing ATPgammaS, a catalytic magnesium ion and an ordered water molecule. Combining the crystal structures of Spa47-ATPgammaS and unliganded Spa47, we propose conformational changes in Spa47 associated with ATP binding, the binding of ATP induces a conformational change of a highly conserved luminal loop, facilitating ATP hydrolysis by the Spa47 ATPase. Additionally, we identified a specific hydrogen bond critical for ATP recognition and demonstrated that, while ATPgammaS is an ideal analog for probing ATP binding, AMPPNP is a poor ATP mimic. Our findings provide structural insight pertinent for inhibitor design.
		+
		+	Structural Insight Into Conformational Changes Induced by ATP Binding in a Type III Secretion-Associated ATPase From Shigella flexneri.,Gao X, Mu Z, Yu X, Qin B, Wojdyla J, Wang M, Cui S Front Microbiol. 2018 Jul 2;9:1468. doi: 10.3389/fmicb.2018.01468. eCollection, 2018. PMID:30013545<ref>PMID:30013545</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ybi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Shigella paradysenteriae weldin 1927]]		[[Category: Shigella paradysenteriae weldin 1927]]
		+	[[Category: Large Structures]]
	[[Category: Cui, S]]		[[Category: Cui, S]]
	[[Category: Gao, X P]]		[[Category: Gao, X P]]

OCA at 06:08, 11 July 2018

OCA — Wed, 11 Jul 2018 06:08:18 GMT

←Older revision		Revision as of 06:08, 11 July 2018
Line 3:		Line 3:
	<StructureSection load='5ybi' size='340' side='right' caption='[[5ybi]], [[Resolution\|resolution]] 2.27Å' scene=''>		<StructureSection load='5ybi' size='340' side='right' caption='[[5ybi]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ybi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YBI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ybi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YBI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2obm\|2obm]], [[5ybh\|5ybh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2obm\|2obm]], [[5ybh\|5ybh]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">spaL, mxiB, spa47, CP0149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 "Shigella paradysenteriae" Weldin 1927])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/H(+)-transporting_two-sector_ATPase H(+)-transporting two-sector ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.14 3.6.3.14] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/H(+)-transporting_two-sector_ATPase H(+)-transporting two-sector ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.14 3.6.3.14] </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=5ybi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybi OCA], [http://pdbe.org/5ybi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ybi RCSB], [http://www.ebi.ac.uk/pdbsum/5ybi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybi 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=5ybi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybi OCA], [http://pdbe.org/5ybi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ybi RCSB], [http://www.ebi.ac.uk/pdbsum/5ybi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybi ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Shigella paradysenteriae weldin 1927]]
	[[Category: Cui, S]]		[[Category: Cui, S]]
	[[Category: Gao, X P]]		[[Category: Gao, X P]]

OCA at 05:43, 20 June 2018

OCA — Wed, 20 Jun 2018 05:43:21 GMT

←Older revision		Revision as of 05:43, 20 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ybi ~~is ON HOLD until Paper Publication~~	+	==Structure of the bacterial pathogens ATPase with substrate AMPPNP==
-		+	<StructureSection load='5ybi' size='340' side='right' caption='[[5ybi]], [[Resolution\|resolution]] 2.27Å' scene=''>
-	~~Authors~~: ~~Mu, Z~~.X.~~, Gao, X~~.P., ~~Cui~~, S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ybi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YBI FirstGlance]. <br>
-	~~Description~~: ~~Structure of the bacterial pathogens~~ ATPase with ~~substrate AMPPNP~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	[[~~Category~~: ~~Gao~~, X.P]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2obm\|2obm]], [[5ybh\|5ybh]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/H(+)-transporting_two-sector_ATPase H(+)-transporting two-sector ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.14 3.6.3.14] </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=5ybi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybi OCA], [http://pdbe.org/5ybi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ybi RCSB], [http://www.ebi.ac.uk/pdbsum/5ybi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybi ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SPAL_SHIFL SPAL_SHIFL]] Required for surface presentation of invasion plasmid antigens. Probable catalytic subunit of a protein translocase. Required for invasion and for secretion of the three IPA proteins.
		+	__TOC__
		+	</StructureSection>
	[[Category: Cui, S]]		[[Category: Cui, S]]
-	[[Category: Mu, Z.X]]	+	[[Category: Gao, X P]]
		+	[[Category: Mu, Z X]]
		+	[[Category: Amppnp]]
		+	[[Category: Atpase]]
		+	[[Category: Hexamer]]
		+	[[Category: Hydrolase]]
		+	[[Category: T3ss]]

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

OCA — Wed, 27 Sep 2017 16:22:30 GMT

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

←Older revision

Revision as of 16:22, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ybi is ON HOLD until Paper Publication Authors: Mu, Z.X., Gao, X.P., Cui, S. Description: Structure of the bacterial pathogens ATPase with substra...

OCA — Wed, 27 Sep 2017 16:22:29 GMT

New page: '''Unreleased structure''' The entry 5ybi is ON HOLD until Paper Publication Authors: Mu, Z.X., Gao, X.P., Cui, S. Description: Structure of the bacterial pathogens ATPase with substra...

New page

'''Unreleased structure'''

The entry 5ybi is ON HOLD until Paper Publication

Authors: Mu, Z.X., Gao, X.P., Cui, S.

Description: Structure of the bacterial pathogens ATPase with substrate AMPPNP
[[Category: Unreleased Structures]]
[[Category: Gao, X.P]]
[[Category: Cui, S]]
[[Category: Mu, Z.X]]