1kmd - Revision history

OCA at 08:42, 22 May 2024

OCA — Wed, 22 May 2024 08:42:02 GMT

←Older revision		Revision as of 08:42, 22 May 2024
Line 19:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kmd ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kmd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	PX domains have been recently found to act as phosphoinositide binding modules. In the yeast SNARE protein Vam7p, the PX domain binds to PtdIns(3)P and is required for vacuolar targeting. To gain insight into how PX domains function, the solution structure of the ligand-free Vam7p PX domain has been determined by NMR spectroscopy. The Vam7p PX domain has the same overall alpha/beta fold observed in the structures of the ligand-free p47(phox) PX domain and the PtdIns(3)P-bound p40(phox) PX domain, exhibiting several similarities and differences with these two PX domains. Most striking is the similarity between the Vam7p and p40(phox) PX domains in a subset of secondary structure elements despite the low level of sequence identity between them, suggesting that these elements form a conserved core in the PX domain fold. These similarities and the observation that a putative PtdIns(3)P binding site is already formed in the apo Vam7p PX domains suggest that ligand binding does not induce major conformational changes, contrary to what was previously thought. The proposed ligand binding site of the Vam7p PX domain includes basic side chains from the conserved structural core that also participate in PtdIns(3)P binding to the p40(phox) PX domain, and basic side chains from a variable loop that probably inserts into the membrane. These results indicate that PX domains contain a combination of conserved and variable features that allow them to have a common function and at the same time exhibit distinct specificities, mechanisms of regulation, or modes of interaction with effector molecules.
		+
		+	Solution structure of the Vam7p PX domain.,Lu J, Garcia J, Dulubova I, Sudhof TC, Rizo J Biochemistry. 2002 May 14;41(19):5956-62. PMID:11993989<ref>PMID:11993989</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1kmd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:01, 3 April 2024

OCA — Wed, 03 Apr 2024 08:01:58 GMT

←Older revision		Revision as of 08:01, 3 April 2024
Line 1:		Line 1:

	==SOLUTION STRUCTURE OF THE VAM7P PX DOMAIN==		==SOLUTION STRUCTURE OF THE VAM7P PX DOMAIN==
-	<StructureSection load='1kmd' size='340' side='right'caption='[[1kmd~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='1kmd' size='340' side='right'caption='[[1kmd]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kmd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KMD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kmd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KMD FirstGlance]. <br>
-	</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=1kmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kmd OCA], [https://pdbe.org/1kmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kmd RCSB], [https://www.ebi.ac.uk/pdbsum/1kmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kmd ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1kmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kmd OCA], [https://pdbe.org/1kmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kmd RCSB], [https://www.ebi.ac.uk/pdbsum/1kmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kmd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/VAM7_YEAST VAM7_YEAST]] Essential for proper morphogenesis of the vacuole. May exist as structural reinforcement on the surface of the vacuolar membrane and be required for maintenance against rupture by osmotic pressure.	+	[https://www.uniprot.org/uniprot/VAM7_YEAST VAM7_YEAST] Essential for proper morphogenesis of the vacuole. May exist as structural reinforcement on the surface of the vacuolar membrane and be required for maintenance against rupture by osmotic pressure.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kmd ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kmd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	PX domains have been recently found to act as phosphoinositide binding modules. In the yeast SNARE protein Vam7p, the PX domain binds to PtdIns(3)P and is required for vacuolar targeting. To gain insight into how PX domains function, the solution structure of the ligand-free Vam7p PX domain has been determined by NMR spectroscopy. The Vam7p PX domain has the same overall alpha/beta fold observed in the structures of the ligand-free p47(phox) PX domain and the PtdIns(3)P-bound p40(phox) PX domain, exhibiting several similarities and differences with these two PX domains. Most striking is the similarity between the Vam7p and p40(phox) PX domains in a subset of secondary structure elements despite the low level of sequence identity between them, suggesting that these elements form a conserved core in the PX domain fold. These similarities and the observation that a putative PtdIns(3)P binding site is already formed in the apo Vam7p PX domains suggest that ligand binding does not induce major conformational changes, contrary to what was previously thought. The proposed ligand binding site of the Vam7p PX domain includes basic side chains from the conserved structural core that also participate in PtdIns(3)P binding to the p40(phox) PX domain, and basic side chains from a variable loop that probably inserts into the membrane. These results indicate that PX domains contain a combination of conserved and variable features that allow them to have a common function and at the same time exhibit distinct specificities, mechanisms of regulation, or modes of interaction with effector molecules.
-
-	Solution structure of the Vam7p PX domain.,Lu J, Garcia J, Dulubova I, Sudhof TC, Rizo J Biochemistry. 2002 May 14;41(19):5956-62. PMID:11993989<ref>PMID:11993989</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1kmd" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dulubova, I]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Garcia, J]]	+	[[Category: Dulubova I]]
-	[[Category: Lu, J]]	+	[[Category: Garcia J]]
-	[[Category: Rizo, J]]	+	[[Category: Lu J]]
-	[[Category: Sudhof~~, T C]]~~	+	[[Category: Rizo J]]
-	~~[[Category: Endocytosis-exocytosis complex]]~~	+	[[Category: Sudhof TC]]
-	~~[[Category: Phosphoinositide binding]]~~	+
-	~~[[Category: Px domain]]~~	+
-	~~[[Category: Vam7p~~]]	+

OCA at 06:33, 18 August 2021

OCA — Wed, 18 Aug 2021 06:33:18 GMT

←Older revision		Revision as of 06:33, 18 August 2021
Line 3:		Line 3:
	<StructureSection load='1kmd' size='340' side='right'caption='[[1kmd]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1kmd' size='340' side='right'caption='[[1kmd]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kmd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KMD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kmd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KMD 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=1kmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kmd OCA], [~~http~~://pdbe.org/1kmd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kmd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kmd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kmd ProSAT]</span></td></tr>	+	</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=1kmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kmd OCA], [https://pdbe.org/1kmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kmd RCSB], [https://www.ebi.ac.uk/pdbsum/1kmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kmd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/VAM7_YEAST VAM7_YEAST]] Essential for proper morphogenesis of the vacuole. May exist as structural reinforcement on the surface of the vacuolar membrane and be required for maintenance against rupture by osmotic pressure.	+	[[https://www.uniprot.org/uniprot/VAM7_YEAST VAM7_YEAST]] Essential for proper morphogenesis of the vacuole. May exist as structural reinforcement on the surface of the vacuolar membrane and be required for maintenance against rupture by osmotic pressure.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:59, 6 November 2019

OCA — Wed, 06 Nov 2019 08:59:37 GMT

←Older revision		Revision as of 08:59, 6 November 2019
Line 1:		Line 1:

	==SOLUTION STRUCTURE OF THE VAM7P PX DOMAIN==		==SOLUTION STRUCTURE OF THE VAM7P PX DOMAIN==
-	<StructureSection load='1kmd' size='340' side='right' caption='[[1kmd]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='1kmd' size='340' side='right'caption='[[1kmd]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kmd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KMD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kmd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KMD FirstGlance]. <br>
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Dulubova, I]]		[[Category: Dulubova, I]]
	[[Category: Garcia, J]]		[[Category: Garcia, J]]

OCA at 21:10, 24 January 2018

OCA — Wed, 24 Jan 2018 21:10:48 GMT

←Older revision		Revision as of 21:10, 24 January 2018
Line 1:		Line 1:
		+
	==SOLUTION STRUCTURE OF THE VAM7P PX DOMAIN==		==SOLUTION STRUCTURE OF THE VAM7P PX DOMAIN==
	<StructureSection load='1kmd' size='340' side='right' caption='[[1kmd]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1kmd' size='340' side='right' caption='[[1kmd]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kmd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KMD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kmd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KMD 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=1kmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kmd OCA], [http://pdbe.org/1kmd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kmd RCSB], [http://www.ebi.ac.uk/pdbsum/1kmd PDBsum]</span></td></tr>	+	</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=1kmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kmd OCA], [http://pdbe.org/1kmd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kmd RCSB], [http://www.ebi.ac.uk/pdbsum/1kmd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kmd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/km/1kmd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/km/1kmd_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 23:57, 7 February 2016

OCA — Sun, 07 Feb 2016 23:57:45 GMT

←Older revision		Revision as of 23:57, 7 February 2016
Line 15:		Line 15:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kmd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:02, 10 September 2015

OCA — Thu, 10 Sep 2015 06:02:16 GMT

←Older revision		Revision as of 06:02, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1kmd' size='340' side='right' caption='[[1kmd]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1kmd' size='340' side='right' caption='[[1kmd]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kmd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KMD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kmd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KMD 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=1kmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kmd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kmd RCSB], [http://www.ebi.ac.uk/pdbsum/1kmd PDBsum]</span></td></tr>	+	</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=1kmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kmd OCA], [http://pdbe.org/1kmd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kmd RCSB], [http://www.ebi.ac.uk/pdbsum/1kmd PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 25:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1kmd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: Dulubova, I]]		[[Category: Dulubova, I]]
	[[Category: Garcia, J]]		[[Category: Garcia, J]]

OCA at 19:06, 24 December 2014

OCA — Wed, 24 Dec 2014 19:06:46 GMT

←Older revision		Revision as of 19:06, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kmd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KMD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kmd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KMD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kmd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kmd RCSB], [http://www.ebi.ac.uk/pdbsum/1kmd PDBsum]</span></td></tr>	+	</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=1kmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kmd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kmd RCSB], [http://www.ebi.ac.uk/pdbsum/1kmd PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VAM7_YEAST VAM7_YEAST]] Essential for proper morphogenesis of the vacuole. May exist as structural reinforcement on the surface of the vacuolar membrane and be required for maintenance against rupture by osmotic pressure.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Dulubova, I.]]	+	[[Category: Dulubova, I]]
-	[[Category: Garcia, J.]]	+	[[Category: Garcia, J]]
-	[[Category: Lu, J.]]	+	[[Category: Lu, J]]
-	[[Category: Rizo, J.]]	+	[[Category: Rizo, J]]
-	[[Category: Sudhof, T C.]]	+	[[Category: Sudhof, T C]]
	[[Category: Endocytosis-exocytosis complex]]		[[Category: Endocytosis-exocytosis complex]]
	[[Category: Phosphoinositide binding]]		[[Category: Phosphoinositide binding]]
	[[Category: Px domain]]		[[Category: Px domain]]
	[[Category: Vam7p]]		[[Category: Vam7p]]

OCA at 10:45, 28 September 2014

OCA — Sun, 28 Sep 2014 10:45:41 GMT

←Older revision		Revision as of 10:45, 28 September 2014
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-	[[~~Image~~:1kmd.~~png\|left~~\|200px]]	+	==SOLUTION STRUCTURE OF THE VAM7P PX DOMAIN==
		+	<StructureSection load='1kmd' size='340' side='right' caption='[[1kmd]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kmd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KMD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kmd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kmd RCSB], [http://www.ebi.ac.uk/pdbsum/1kmd PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/km/1kmd_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	PX domains have been recently found to act as phosphoinositide binding modules. In the yeast SNARE protein Vam7p, the PX domain binds to PtdIns(3)P and is required for vacuolar targeting. To gain insight into how PX domains function, the solution structure of the ligand-free Vam7p PX domain has been determined by NMR spectroscopy. The Vam7p PX domain has the same overall alpha/beta fold observed in the structures of the ligand-free p47(phox) PX domain and the PtdIns(3)P-bound p40(phox) PX domain, exhibiting several similarities and differences with these two PX domains. Most striking is the similarity between the Vam7p and p40(phox) PX domains in a subset of secondary structure elements despite the low level of sequence identity between them, suggesting that these elements form a conserved core in the PX domain fold. These similarities and the observation that a putative PtdIns(3)P binding site is already formed in the apo Vam7p PX domains suggest that ligand binding does not induce major conformational changes, contrary to what was previously thought. The proposed ligand binding site of the Vam7p PX domain includes basic side chains from the conserved structural core that also participate in PtdIns(3)P binding to the p40(phox) PX domain, and basic side chains from a variable loop that probably inserts into the membrane. These results indicate that PX domains contain a combination of conserved and variable features that allow them to have a common function and at the same time exhibit distinct specificities, mechanisms of regulation, or modes of interaction with effector molecules.

-	~~{{STRUCTURE_1kmd\| PDB=1kmd \| SCENE= }}~~	+	Solution structure of the Vam7p PX domain.,Lu J, Garcia J, Dulubova I, Sudhof TC, Rizo J Biochemistry. 2002 May 14;41(19):5956-62. PMID:11993989<ref>PMID:11993989</ref>

-	~~===SOLUTION STRUCTURE OF THE VAM7P PX DOMAIN===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11993989}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1kmd]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1KMD OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:011993989<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Dulubova, I.]]		[[Category: Dulubova, I.]]

OCA: Protected "1kmd" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 20:31:17 GMT

Protected "1kmd" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:31, 5 December 2012