7viq - Revision history

OCA at 07:23, 3 April 2024

OCA — Wed, 03 Apr 2024 07:23:07 GMT

←Older revision		Revision as of 07:23, 3 April 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7viq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VIQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[7viq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VIQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</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]] 1.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</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=7viq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7viq OCA], [https://pdbe.org/7viq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7viq RCSB], [https://www.ebi.ac.uk/pdbsum/7viq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7viq 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=7viq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7viq OCA], [https://pdbe.org/7viq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7viq RCSB], [https://www.ebi.ac.uk/pdbsum/7viq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7viq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/FRIL_HORSE FRIL_HORSE] Stores iron in a soluble, non-toxic, readily available form. Important for iron homeostasis. Iron is taken up in the ferrous form and deposited as ferric hydroxides after oxidation. Also plays a role in delivery of iron to cells. Mediates iron uptake in capsule cells of the developing kidney (By similarity).		[https://www.uniprot.org/uniprot/FRIL_HORSE FRIL_HORSE] Stores iron in a soluble, non-toxic, readily available form. Important for iron homeostasis. Iron is taken up in the ferrous form and deposited as ferric hydroxides after oxidation. Also plays a role in delivery of iron to cells. Mediates iron uptake in capsule cells of the developing kidney (By similarity).
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Water-soluble and biocompatible protein-protected gold nanoclusters (Au NCs) hold great promise for numerous applications. However, design and precise regulation of their structure at an atomic level remain challenging. Herein, we have engineered and constructed a gold clustering site at the 4-fold symmetric axis channel of the apo-ferritin cage. Using a series of X-ray crystal structures, we evaluated the stepwise accumulation process of Au ions into the cage and the formation of a multinuclear Au cluster in our designed cavity. We also disclosed the role of key residues in the metal accumulation process. X-ray crystal structures in combination with quantum chemical (QC) calculation revealed a unique Au clustering site with up to 12 Au atoms positions in the cavity. Moreover, the structure of the gold nanocluster was precisely tuned by the dosage of the Au precursor. As the gold concentration increases, the number of Au atoms position at the clustering site increases from 8 to 12, and a structural rearrangement was observed at a higher Au concentration. Furthermore, the binding affinity order of the four Au binding sites on apo-ferritin was unveiled with a stepwise increase of Au precursor concentration.

-	Design of a gold clustering site in an engineered apo-ferritin cage.,Lu C, Maity B, Peng X, Ito N, Abe S, Sheng X, Ueno T, Lu D Commun Chem. 2022 Mar 21;5(1):39. doi: 10.1038/s42004-022-00651-1. PMID:36697940<ref>PMID:36697940</ref>	+	==See Also==
-		+	*[[Ferritin 3D structures\|Ferritin 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 7viq" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:58, 8 February 2023

OCA — Wed, 08 Feb 2023 06:58:19 GMT

←Older revision		Revision as of 06:58, 8 February 2023
Line 1:		Line 1:

	==Crystal structure of Au(50EQ)-apo-R168H/L169C-rHLFr==		==Crystal structure of Au(50EQ)-apo-R168H/L169C-rHLFr==
-	<StructureSection load='7viq' size='340' side='right'caption='[[7viq]]' scene=''>	+	<StructureSection load='7viq' size='340' side='right'caption='[[7viq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VIQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7viq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VIQ 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=7viq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7viq OCA], [https://pdbe.org/7viq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7viq RCSB], [https://www.ebi.ac.uk/pdbsum/7viq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7viq ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</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=7viq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7viq OCA], [https://pdbe.org/7viq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7viq RCSB], [https://www.ebi.ac.uk/pdbsum/7viq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7viq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/FRIL_HORSE FRIL_HORSE] Stores iron in a soluble, non-toxic, readily available form. Important for iron homeostasis. Iron is taken up in the ferrous form and deposited as ferric hydroxides after oxidation. Also plays a role in delivery of iron to cells. Mediates iron uptake in capsule cells of the developing kidney (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Water-soluble and biocompatible protein-protected gold nanoclusters (Au NCs) hold great promise for numerous applications. However, design and precise regulation of their structure at an atomic level remain challenging. Herein, we have engineered and constructed a gold clustering site at the 4-fold symmetric axis channel of the apo-ferritin cage. Using a series of X-ray crystal structures, we evaluated the stepwise accumulation process of Au ions into the cage and the formation of a multinuclear Au cluster in our designed cavity. We also disclosed the role of key residues in the metal accumulation process. X-ray crystal structures in combination with quantum chemical (QC) calculation revealed a unique Au clustering site with up to 12 Au atoms positions in the cavity. Moreover, the structure of the gold nanocluster was precisely tuned by the dosage of the Au precursor. As the gold concentration increases, the number of Au atoms position at the clustering site increases from 8 to 12, and a structural rearrangement was observed at a higher Au concentration. Furthermore, the binding affinity order of the four Au binding sites on apo-ferritin was unveiled with a stepwise increase of Au precursor concentration.
		+
		+	Design of a gold clustering site in an engineered apo-ferritin cage.,Lu C, Maity B, Peng X, Ito N, Abe S, Sheng X, Ueno T, Lu D Commun Chem. 2022 Mar 21;5(1):39. doi: 10.1038/s42004-022-00651-1. PMID:36697940<ref>PMID:36697940</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7viq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Equus caballus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Abe S]]		[[Category: Abe S]]

OCA at 05:30, 8 June 2022

OCA — Wed, 08 Jun 2022 05:30:55 GMT

←Older revision		Revision as of 05:30, 8 June 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7viq ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of Au(50EQ)-apo-R168H/L169C-rHLFr==
-		+	<StructureSection load='7viq' size='340' side='right'caption='[[7viq]]' scene=''>
-	~~Authors~~: ~~Lu, C~~.~~, Peng, X~~., ~~Maity, B~~., ~~Ito, N~~., ~~Abe, S~~., ~~Ueno, T~~., ~~Lu, D~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VIQ FirstGlance]. <br>
-	~~Description: Crystal structure of Au(50EQ)-apo-R168H~~/~~L169C-rHLFr~~	+	</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=7viq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7viq OCA], [https://pdbe.org/7viq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7viq RCSB], [https://www.ebi.ac.uk/pdbsum/7viq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7viq ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Maity, B~~]]	+	__TOC__
-	[[Category: ~~Abe, S~~]]	+	</StructureSection>
-	[[Category: ~~Peng, X~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ueno, T~~]]	+	[[Category: Abe S]]
-	[[Category: ~~Ito, N~~]]	+	[[Category: Ito N]]
-	[[Category: ~~Lu, D~~]]	+	[[Category: Lu C]]
-	[[Category: ~~Lu, C~~]]	+	[[Category: Lu D]]
		+	[[Category: Maity B]]
		+	[[Category: Peng X]]
		+	[[Category: Ueno T]]

OCA at 12:22, 29 December 2021

OCA — Wed, 29 Dec 2021 12:22:05 GMT

←Older revision		Revision as of 12:22, 29 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7viq is ON HOLD	+	The entry 7viq is ON HOLD until Paper Publication

	Authors: Lu, C., Peng, X., Maity, B., Ito, N., Abe, S., Ueno, T., Lu, D.		Authors: Lu, C., Peng, X., Maity, B., Ito, N., Abe, S., Ueno, T., Lu, D.

OCA: Protected "7viq" [edit=sysop:move=sysop]

OCA — Wed, 06 Oct 2021 04:22:37 GMT

Protected "7viq" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:22, 6 October 2021

OCA: New page: '''Unreleased structure''' The entry 7viq is ON HOLD Authors: Lu, C., Peng, X., Maity, B., Ito, N., Abe, S., Ueno, T., Lu, D. Description: Crystal structure of Au(50EQ)-apo-R168H/L169C...

OCA — Wed, 06 Oct 2021 04:22:36 GMT

New page: '''Unreleased structure''' The entry 7viq is ON HOLD Authors: Lu, C., Peng, X., Maity, B., Ito, N., Abe, S., Ueno, T., Lu, D. Description: Crystal structure of Au(50EQ)-apo-R168H/L169C...

New page

'''Unreleased structure'''

The entry 7viq is ON HOLD

Authors: Lu, C., Peng, X., Maity, B., Ito, N., Abe, S., Ueno, T., Lu, D.

Description: Crystal structure of Au(50EQ)-apo-R168H/L169C-rHLFr
[[Category: Unreleased Structures]]
[[Category: Maity, B]]
[[Category: Abe, S]]
[[Category: Peng, X]]
[[Category: Ueno, T]]
[[Category: Ito, N]]
[[Category: Lu, D]]
[[Category: Lu, C]]