5kk4 - Revision history

OCA at 10:02, 27 September 2023

2023-09-27T10:02:24Z

←Older revision		Revision as of 10:02, 27 September 2023
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	<StructureSection load='5kk4' size='340' side='right'caption='[[5kk4]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5kk4' size='340' side='right'caption='[[5kk4]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kk4]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Nicotiana_suaveolens_x_nicotiana_tabacum~~ Nicotiana suaveolens x ~~nicotiana~~ tabacum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KK4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KK4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kk4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Nicotiana_suaveolens_x_Nicotiana_tabacum Nicotiana suaveolens x Nicotiana tabacum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KK4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=44E:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+DIHEXANOATE'>44E</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.7Å</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=5kk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kk4 OCA], [~~http~~://pdbe.org/5kk4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kk4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kk4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kk4 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=44E:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+DIHEXANOATE'>44E</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5kk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kk4 OCA], [https://pdbe.org/5kk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kk4 RCSB], [https://www.ebi.ac.uk/pdbsum/5kk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kk4 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DEF_NICSU DEF_NICSU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Nicotiana suaveolens x ~~nicotiana~~ tabacum]]	+	[[Category: Nicotiana suaveolens x Nicotiana tabacum]]
-	[[Category: Hulett~~, M D~~]]	+	[[Category: Hulett MD]]
-	[[Category: Kvansakul, M]]	+	[[Category: Kvansakul M]]
-	[[Category: Lay~~, F T]]~~	+	[[Category: Lay FT]]
-	~~[[Category: Antimicrobial protein]]~~	+
-	~~[[Category: Defensin]]~~	+
-	~~[[Category: Oligomer]]~~	+
-	~~[[Category: Phosphatidic acid]]~~	+
-	~~[[Category: Phospholipid~~]]	+

OCA at 09:01, 1 January 2020

2020-01-01T09:01:23Z

←Older revision		Revision as of 09:01, 1 January 2020
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	==Crystal Structure of the Plant Defensin NsD7 bound to Phosphatidic Acid==		==Crystal Structure of the Plant Defensin NsD7 bound to Phosphatidic Acid==
-	<StructureSection load='5kk4' size='340' side='right' caption='[[5kk4]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5kk4' size='340' side='right'caption='[[5kk4]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kk4]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KK4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KK4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kk4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Nicotiana_suaveolens_x_nicotiana_tabacum Nicotiana suaveolens x nicotiana tabacum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KK4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KK4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=44E:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+DIHEXANOATE'>44E</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=44E:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+DIHEXANOATE'>44E</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5kk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kk4 OCA], [http://pdbe.org/5kk4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kk4 RCSB], [http://www.ebi.ac.uk/pdbsum/5kk4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kk4 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=5kk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kk4 OCA], [http://pdbe.org/5kk4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kk4 RCSB], [http://www.ebi.ac.uk/pdbsum/5kk4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kk4 ProSAT]</span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 5kk4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5kk4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Defensin 3D structures\|Defensin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Nicotiana suaveolens x nicotiana tabacum]]
	[[Category: Hulett, M D]]		[[Category: Hulett, M D]]
	[[Category: Kvansakul, M]]		[[Category: Kvansakul, M]]

OCA at 21:33, 5 October 2016

2016-10-05T21:33:25Z

←Older revision		Revision as of 21:33, 5 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kk4 is ~~ON HOLD~~	+	==Crystal Structure of the Plant Defensin NsD7 bound to Phosphatidic Acid==
		+	<StructureSection load='5kk4' size='340' side='right' caption='[[5kk4]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kk4]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KK4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KK4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=44E:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+DIHEXANOATE'>44E</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5kk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kk4 OCA], [http://pdbe.org/5kk4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kk4 RCSB], [http://www.ebi.ac.uk/pdbsum/5kk4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kk4 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Defensins are cationic antimicrobial peptides that serve as important components of host innate immune defenses, often by targeting cell membranes of pathogens. Oligomerization of defensins has been linked to their antimicrobial activity; however, the molecular basis underpinning this process remains largely unclear. Here we show that the plant defensin NsD7 targets the phospholipid phosphatidic acid (PA) to form oligomeric complexes that permeabilize PA-containing membranes. The crystal structure of the NsD7-PA complex reveals a striking double helix of two right-handed coiled oligomeric defensin fibrils, the assembly of which is dependent upon the interaction with PA at the interface between NsD7 dimers. Using site-directed mutagenesis, we demonstrate that key residues in this PA-binding site are required for PA-mediated NsD7 oligomerization and coil formation, as well as permeabilization of PA-containing liposomes. These data suggest that multiple lipids can be targeted to induce oligomerization of defensins during membrane permeabilization and demonstrate the existence of a "phospholipid code" that identifies target membranes for defensin-mediated attack as part of a first line of defense across multiple species.

-	~~Authors~~:	+	Binding of phosphatidic acid by NsD7 mediates the formation of helical defensin-lipid oligomeric assemblies and membrane permeabilization.,Kvansakul M, Lay FT, Adda CG, Veneer PK, Baxter AA, Phan TK, Poon IK, Hulett MD Proc Natl Acad Sci U S A. 2016 Sep 19. pii: 201607855. PMID:27647905<ref>PMID:27647905</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5kk4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hulett, M D]]
		+	[[Category: Kvansakul, M]]
		+	[[Category: Lay, F T]]
		+	[[Category: Antimicrobial protein]]
		+	[[Category: Defensin]]
		+	[[Category: Oligomer]]
		+	[[Category: Phosphatidic acid]]
		+	[[Category: Phospholipid]]

OCA: Protected "5kk4" [edit=sysop:move=sysop]

2016-07-13T00:27:54Z

Protected "5kk4" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:27, 13 July 2016

OCA: New page: '''Unreleased structure''' The entry 5kk4 is ON HOLD Authors: Description: Category: Unreleased Structures

2016-07-13T00:27:52Z

New page: '''Unreleased structure''' The entry 5kk4 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5kk4 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]