6iu9 - Revision history

OCA at 09:53, 22 November 2023

2023-11-22T09:53:07Z

←Older revision		Revision as of 09:53, 22 November 2023
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	<StructureSection load='6iu9' size='340' side='right'caption='[[6iu9]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='6iu9' size='340' side='right'caption='[[6iu9]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6iu9]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Eucgr Eucgr~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IU9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IU9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6iu9]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Eucalyptus_grandis Eucalyptus grandis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IU9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IU9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6iu9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iu9 OCA], [https://pdbe.org/6iu9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6iu9 RCSB], [https://www.ebi.ac.uk/pdbsum/6iu9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6iu9 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=6iu9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iu9 OCA], [https://pdbe.org/6iu9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6iu9 RCSB], [https://www.ebi.ac.uk/pdbsum/6iu9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6iu9 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Eucgr~~]]	+	[[Category: Eucalyptus grandis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ishitani, R]]	+	[[Category: Ishitani R]]
-	[[Category: Kato, T]]	+	[[Category: Kato T]]
-	[[Category: Kumazaki, K]]	+	[[Category: Kumazaki K]]
-	[[Category: Nishizawa, T]]	+	[[Category: Nishizawa T]]
-	[[Category: Nureki, O]]	+	[[Category: Nureki O]]
-	[[Category: Yamashita, K]]	+	[[Category: Yamashita K]]
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Metal transport~~]]	+

OCA at 10:29, 18 March 2021

2021-03-18T10:29:10Z

←Older revision		Revision as of 10:29, 18 March 2021
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	<StructureSection load='6iu9' size='340' side='right'caption='[[6iu9]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='6iu9' size='340' side='right'caption='[[6iu9]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6iu9]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Eucgr Eucgr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IU9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IU9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6iu9]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Eucgr Eucgr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IU9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IU9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6iu9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iu9 OCA], [~~http~~://pdbe.org/6iu9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6iu9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6iu9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6iu9 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=6iu9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iu9 OCA], [https://pdbe.org/6iu9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6iu9 RCSB], [https://www.ebi.ac.uk/pdbsum/6iu9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6iu9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:06, 27 March 2019

2019-03-27T07:06:55Z

←Older revision		Revision as of 07:06, 27 March 2019
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	==Crystal structure of cytoplasmic metal binding domain with iron ions==		==Crystal structure of cytoplasmic metal binding domain with iron ions==
-	<StructureSection load='6iu9' size='340' side='right' caption='[[6iu9]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='6iu9' size='340' side='right'caption='[[6iu9]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6iu9]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Eucgr Eucgr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IU9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IU9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6iu9]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Eucgr Eucgr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IU9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IU9 FirstGlance]. <br>
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Eucgr]]		[[Category: Eucgr]]
		+	[[Category: Large Structures]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]
	[[Category: Kato, T]]		[[Category: Kato, T]]

OCA at 16:02, 27 February 2019

2019-02-27T16:02:06Z

←Older revision		Revision as of 16:02, 27 February 2019
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	<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=6iu9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iu9 OCA], [http://pdbe.org/6iu9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iu9 RCSB], [http://www.ebi.ac.uk/pdbsum/6iu9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iu9 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=6iu9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iu9 OCA], [http://pdbe.org/6iu9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iu9 RCSB], [http://www.ebi.ac.uk/pdbsum/6iu9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iu9 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The iron ion is an essential cofactor in several vital enzymatic reactions, such as DNA replication, oxygen transport, and respiratory and photosynthetic electron transfer chains, but its excess accumulation induces oxidative stress in cells. Vacuolar iron transporter 1 (VIT1) is important for iron homeostasis in plants, by transporting cytoplasmic ferrous ions into vacuoles. Modification of the VIT1 gene leads to increased iron content in crops, which could be used for the treatment of human iron deficiency diseases. Furthermore, a VIT1 from the malaria-causing parasite Plasmodium is considered as a potential drug target for malaria. Here we report the crystal structure of VIT1 from rose gum Eucalyptus grandis, which probably functions as a H(+)-dependent antiporter for Fe(2+) and other transition metal ions. VIT1 adopts a novel protein fold forming a dimer of five membrane-spanning domains, with an ion-translocating pathway constituted by the conserved methionine and carboxylate residues at the dimer interface. The second transmembrane helix protrudes from the lipid membrane by about 40 A and connects to a three-helical bundle, triangular cytoplasmic domain, which binds to the substrate metal ions and stabilizes their soluble form, thus playing an essential role in their transport. These mechanistic insights will provide useful information for the further design of genetically modified crops and the development of anti-malaria drugs.
		+
		+	Crystal structure of plant vacuolar iron transporter VIT1.,Kato T, Kumazaki K, Wada M, Taniguchi R, Nakane T, Yamashita K, Hirata K, Ishitani R, Ito K, Nishizawa T, Nureki O Nat Plants. 2019 Feb 11. pii: 10.1038/s41477-019-0367-2. doi:, 10.1038/s41477-019-0367-2. PMID:30742036<ref>PMID:30742036</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6iu9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:47, 21 February 2019

2019-02-21T08:47:59Z

←Older revision		Revision as of 08:47, 21 February 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6iu9 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of cytoplasmic metal binding domain with iron ions==
-		+	<StructureSection load='6iu9' size='340' side='right' caption='[[6iu9]], [[Resolution\|resolution]] 3.00Å' scene=''>
-	~~Authors~~: ~~Kato~~, T., ~~Nishizawa, T~~., ~~Yamashita, K~~., ~~Kumazaki, K~~., Ishitani, R., ~~Nureki, O.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6iu9]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Eucgr Eucgr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IU9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IU9 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of cytoplasmic metal binding domain with iron ions~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6iu9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iu9 OCA], [http://pdbe.org/6iu9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iu9 RCSB], [http://www.ebi.ac.uk/pdbsum/6iu9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iu9 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Eucgr]]
		+	[[Category: Ishitani, R]]
		+	[[Category: Kato, T]]
		+	[[Category: Kumazaki, K]]
		+	[[Category: Nishizawa, T]]
	[[Category: Nureki, O]]		[[Category: Nureki, O]]
-	[[Category: Kumazaki, K]]
	[[Category: Yamashita, K]]		[[Category: Yamashita, K]]
-	[[Category: ~~Nishizawa, T~~]]	+	[[Category: Membrane protein]]
-	[[Category: ~~Kato, T]]~~	+	[[Category: Metal transport]]
-	~~[[Category: Ishitani, R~~]]	+

OCA at 10:21, 16 January 2019

2019-01-16T10:21:43Z

←Older revision		Revision as of 10:21, 16 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6iu9 is ON HOLD	+	The entry 6iu9 is ON HOLD until Paper Publication

	Authors: Kato, T., Nishizawa, T., Yamashita, K., Kumazaki, K., Ishitani, R., Nureki, O.		Authors: Kato, T., Nishizawa, T., Yamashita, K., Kumazaki, K., Ishitani, R., Nureki, O.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Nureki, O]]		[[Category: Nureki, O]]
		+	[[Category: Kumazaki, K]]
	[[Category: Yamashita, K]]		[[Category: Yamashita, K]]
	[[Category: Nishizawa, T]]		[[Category: Nishizawa, T]]
	[[Category: Kato, T]]		[[Category: Kato, T]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]
-	[[Category: Kumazaki, K]]

OCA: Protected "6iu9" [edit=sysop:move=sysop]

2018-12-05T05:11:26Z

Protected "6iu9" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:11, 5 December 2018

OCA: New page: '''Unreleased structure''' The entry 6iu9 is ON HOLD Authors: Kato, T., Nishizawa, T., Yamashita, K., Kumazaki, K., Ishitani, R., Nureki, O. Description: Crystal structure of cytoplasm...

2018-12-05T05:11:25Z

New page: '''Unreleased structure''' The entry 6iu9 is ON HOLD Authors: Kato, T., Nishizawa, T., Yamashita, K., Kumazaki, K., Ishitani, R., Nureki, O. Description: Crystal structure of cytoplasm...

New page

'''Unreleased structure'''

The entry 6iu9 is ON HOLD

Authors: Kato, T., Nishizawa, T., Yamashita, K., Kumazaki, K., Ishitani, R., Nureki, O.

Description: Crystal structure of cytoplasmic metal binding domain with iron ions
[[Category: Unreleased Structures]]
[[Category: Nureki, O]]
[[Category: Yamashita, K]]
[[Category: Nishizawa, T]]
[[Category: Kato, T]]
[[Category: Ishitani, R]]
[[Category: Kumazaki, K]]