6nsj - Revision history

OCA at 09:21, 20 March 2024

OCA — Wed, 20 Mar 2024 09:21:52 GMT

←Older revision		Revision as of 09:21, 20 March 2024
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	<SX load='6nsj' size='340' side='right' viewer='molstar' caption='[[6nsj]], [[Resolution\|resolution]] 2.70Å' scene=''>		<SX load='6nsj' size='340' side='right' viewer='molstar' caption='[[6nsj]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nsj]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Campylobacter_pylori_j99 Campylobacter~~ pylori ~~j99~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NSJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6NSJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nsj]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_J99 Helicobacter pylori J99]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NSJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NSJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=XP4:1~~,2~~-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE'>XP4</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]] 2.7Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ureI, jhp_0066 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=85963 Campylobacter pylori J99])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XP4:1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE'>XP4</scene></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=6nsj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nsj OCA], [~~http~~://pdbe.org/6nsj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6nsj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6nsj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6nsj 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=6nsj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nsj OCA], [https://pdbe.org/6nsj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nsj RCSB], [https://www.ebi.ac.uk/pdbsum/6nsj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nsj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UREI_HELPJ UREI_HELPJ]] Functions as a specific, H(+)-activated urea channel that increases the rate of urea entry into the cytoplasm, resulting in activation of cytoplasmic urease at acidic medium pH. Is essential for H.pylori gastric survival and colonization. Is necessary for the adaptation of urease activity to the extracellular pH, as in the presence of urea, UreI rapidly enhances the production of ammonia in the extracellular medium when the pH of the medium was decreased to pH5 or below (By similarity).	+	[https://www.uniprot.org/uniprot/UREI_HELPJ UREI_HELPJ] Functions as a specific, H(+)-activated urea channel that increases the rate of urea entry into the cytoplasm, resulting in activation of cytoplasmic urease at acidic medium pH. Is essential for H.pylori gastric survival and colonization. Is necessary for the adaptation of urease activity to the extracellular pH, as in the presence of urea, UreI rapidly enhances the production of ammonia in the extracellular medium when the pH of the medium was decreased to pH5 or below (By similarity).
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The urea channel of Helicobacter pylori (HpUreI) is an ideal drug target for preventing gastric cancer but incomplete understanding of its gating mechanism has hampered development of inhibitors for the eradication of H. pylori. Here, we present the cryo-EM structures of HpUreI in closed and open conformations, both at a resolution of 2.7 A. Our hexameric structures of this small membrane protein (~21 kDa/protomer) resolve its periplasmic loops and carboxyl terminus that close and open the channel, and define a gating mechanism that is pH dependent and requires cooperativity between protomers in the hexamer. Gating is further associated with well-resolved changes in the channel-lining residues that modify the shape and length of the urea pore. Site-specific mutations in the periplasmic domain and urea pore identified key residues important for channel function. Drugs blocking the urea pore based on our structures should lead to a new strategy for H. pylori eradication.	+

-	pH-dependent gating mechanism of the Helicobacter pylori urea channel revealed by cryo-EM.,Cui Y, Zhou K, Strugatsky D, Wen Y, Sachs G, Zhou ZH, Munson K Sci Adv. 2019 Mar 20;5(3):eaav8423. doi: 10.1126/sciadv.aav8423. eCollection 2019, Mar. PMID:30906870<ref>PMID:30906870</ref>	+	==See Also==
-		+	*[[Urease accessory protein 3D structures\|Urease accessory protein 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6nsj" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: ~~Campylobacter~~ pylori ~~j99~~]]	+	[[Category: Helicobacter pylori J99]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cui~~, Y X~~]]	+	[[Category: Cui YX]]
-	[[Category: Munson, K]]	+	[[Category: Munson K]]
-	[[Category: Sachs, G]]	+	[[Category: Sachs G]]
-	[[Category: Strugatsky, D]]	+	[[Category: Strugatsky D]]
-	[[Category: Wen, Y]]	+	[[Category: Wen Y]]
-	[[Category: Zhou, K]]	+	[[Category: Zhou K]]
-	[[Category: Zhou~~, Z H]]~~	+	[[Category: Zhou ZH]]
-	~~[[Category: Closed state]]~~	+
-	~~[[Category: Helicobacter pylori]]~~	+
-	~~[[Category: Transport protein]]~~	+
-	~~[[Category: Urea channel~~]]	+

OCA at 03:32, 11 April 2020

OCA — Sat, 11 Apr 2020 03:32:22 GMT

←Older revision		Revision as of 03:32, 11 April 2020
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	<SX load='6nsj' size='340' side='right' viewer='molstar' caption='[[6nsj]], [[Resolution\|resolution]] 2.70Å' scene=''>		<SX load='6nsj' size='340' side='right' viewer='molstar' caption='[[6nsj]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nsj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori_j99 Campylobacter pylori j99]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NSJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NSJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nsj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori_j99 Campylobacter pylori j99]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NSJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6NSJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XP4:1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE'>XP4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XP4:1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE'>XP4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ureI, jhp_0066 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85963 Campylobacter pylori J99])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ureI, jhp_0066 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85963 Campylobacter pylori J99])</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=6nsj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nsj OCA], [http://pdbe.org/6nsj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nsj RCSB], [http://www.ebi.ac.uk/pdbsum/6nsj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nsj 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=6nsj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nsj OCA], [http://pdbe.org/6nsj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nsj RCSB], [http://www.ebi.ac.uk/pdbsum/6nsj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nsj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 22:54, 6 March 2020

OCA — Fri, 06 Mar 2020 22:54:44 GMT

←Older revision		Revision as of 22:54, 6 March 2020
Line 1:		Line 1:

	==CryoEM structure of Helicobacter pylori urea channel in closed state==		==CryoEM structure of Helicobacter pylori urea channel in closed state==
-	<~~StructureSection~~ load='6nsj' size='340' side='right'caption='[[6nsj]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<SX load='6nsj' size='340' side='right' viewer='molstar' caption='[[6nsj]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6nsj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori_j99 Campylobacter pylori j99]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NSJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NSJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[6nsj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori_j99 Campylobacter pylori j99]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NSJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NSJ FirstGlance]. <br>
Line 22:		Line 22:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Campylobacter pylori j99]]		[[Category: Campylobacter pylori j99]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 10:36, 4 December 2019

OCA — Wed, 04 Dec 2019 10:36:35 GMT

←Older revision		Revision as of 10:36, 4 December 2019
Line 3:		Line 3:
	<StructureSection load='6nsj' size='340' side='right'caption='[[6nsj]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='6nsj' size='340' side='right'caption='[[6nsj]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nsj]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NSJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NSJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nsj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori_j99 Campylobacter pylori j99]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NSJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NSJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XP4:1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE'>XP4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XP4:1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE'>XP4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ureI, jhp_0066 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85963 Campylobacter pylori J99])</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=6nsj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nsj OCA], [http://pdbe.org/6nsj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nsj RCSB], [http://www.ebi.ac.uk/pdbsum/6nsj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nsj 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=6nsj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nsj OCA], [http://pdbe.org/6nsj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nsj RCSB], [http://www.ebi.ac.uk/pdbsum/6nsj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nsj ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Campylobacter pylori j99]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Cui, Y X]]		[[Category: Cui, Y X]]

OCA at 07:09, 3 April 2019

OCA — Wed, 03 Apr 2019 07:09:27 GMT

←Older revision		Revision as of 07:09, 3 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6nsj is ~~ON HOLD until Paper~~ Publication	+	==CryoEM structure of Helicobacter pylori urea channel in closed state==
		+	<StructureSection load='6nsj' size='340' side='right'caption='[[6nsj]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6nsj]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NSJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NSJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XP4:1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE'>XP4</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=6nsj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nsj OCA], [http://pdbe.org/6nsj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nsj RCSB], [http://www.ebi.ac.uk/pdbsum/6nsj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nsj ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UREI_HELPJ UREI_HELPJ]] Functions as a specific, H(+)-activated urea channel that increases the rate of urea entry into the cytoplasm, resulting in activation of cytoplasmic urease at acidic medium pH. Is essential for H.pylori gastric survival and colonization. Is necessary for the adaptation of urease activity to the extracellular pH, as in the presence of urea, UreI rapidly enhances the production of ammonia in the extracellular medium when the pH of the medium was decreased to pH5 or below (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The urea channel of Helicobacter pylori (HpUreI) is an ideal drug target for preventing gastric cancer but incomplete understanding of its gating mechanism has hampered development of inhibitors for the eradication of H. pylori. Here, we present the cryo-EM structures of HpUreI in closed and open conformations, both at a resolution of 2.7 A. Our hexameric structures of this small membrane protein (~21 kDa/protomer) resolve its periplasmic loops and carboxyl terminus that close and open the channel, and define a gating mechanism that is pH dependent and requires cooperativity between protomers in the hexamer. Gating is further associated with well-resolved changes in the channel-lining residues that modify the shape and length of the urea pore. Site-specific mutations in the periplasmic domain and urea pore identified key residues important for channel function. Drugs blocking the urea pore based on our structures should lead to a new strategy for H. pylori eradication.

-	~~Authors~~:	+	pH-dependent gating mechanism of the Helicobacter pylori urea channel revealed by cryo-EM.,Cui Y, Zhou K, Strugatsky D, Wen Y, Sachs G, Zhou ZH, Munson K Sci Adv. 2019 Mar 20;5(3):eaav8423. doi: 10.1126/sciadv.aav8423. eCollection 2019, Mar. PMID:30906870<ref>PMID:30906870</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6nsj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cui, Y X]]
		+	[[Category: Munson, K]]
		+	[[Category: Sachs, G]]
		+	[[Category: Strugatsky, D]]
		+	[[Category: Wen, Y]]
		+	[[Category: Zhou, K]]
		+	[[Category: Zhou, Z H]]
		+	[[Category: Closed state]]
		+	[[Category: Helicobacter pylori]]
		+	[[Category: Transport protein]]
		+	[[Category: Urea channel]]

OCA at 07:40, 13 February 2019

OCA — Wed, 13 Feb 2019 07:40:05 GMT

←Older revision		Revision as of 07:40, 13 February 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 30 Jan 2019 06:51:41 GMT

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

←Older revision

Revision as of 06:51, 30 January 2019

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

OCA — Wed, 30 Jan 2019 06:51:39 GMT

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

New page

'''Unreleased structure'''

The entry 6nsj is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]