4o79 - Revision history

OCA at 14:54, 8 November 2023

OCA — Wed, 08 Nov 2023 14:54:15 GMT

←Older revision		Revision as of 14:54, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4o79]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O79 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4o79]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O79 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASC:ASCORBIC+ACID'>ASC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 2.003Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASC:ASCORBIC+ACID'>ASC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=4o79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o79 OCA], [https://pdbe.org/4o79 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o79 RCSB], [https://www.ebi.ac.uk/pdbsum/4o79 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o79 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=4o79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o79 OCA], [https://pdbe.org/4o79 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o79 RCSB], [https://www.ebi.ac.uk/pdbsum/4o79 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o79 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:58, 18 January 2023

OCA — Wed, 18 Jan 2023 08:58:57 GMT

←Older revision		Revision as of 08:58, 18 January 2023
Line 1:		Line 1:

	==Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soaked in 1 M L-ascorbate for 10 minutes==		==Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soaked in 1 M L-ascorbate for 10 minutes==
-	<StructureSection load='4o79' size='340' side='right' caption='[[4o79]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='4o79' size='340' side='right'caption='[[4o79]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4o79]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O79 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4O79 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4o79]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O79 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASC:ASCORBIC+ACID'>ASC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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" id="ligandDat"><scene name='pdbligand=ASC:ASCORBIC+ACID'>ASC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4o6y\|4o6y]], [[4o7g\|4o7g]]</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=4o79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o79 OCA], [https://pdbe.org/4o79 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o79 RCSB], [https://www.ebi.ac.uk/pdbsum/4o79 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o79 ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CYB561B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ascorbate_ferrireductase_(transmembrane) Ascorbate ferrireductase (transmembrane)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.16.5.1 1.16.5.1] </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=4o79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o79 OCA], [~~http~~://pdbe.org/4o79 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4o79 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4o79 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4o79 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ACFR2_ARATH ACFR2_ARATH]] Two-heme-containing cytochrome. Catalyzes ascorbate-dependent trans-membrane ferric-chelate reduction (By similarity).	+	[https://www.uniprot.org/uniprot/ACFR2_ARATH ACFR2_ARATH] Two-heme-containing cytochrome. Catalyzes ascorbate-dependent trans-membrane ferric-chelate reduction (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
-	[[Category: Du, M]]	+	[[Category: Large Structures]]
-	[[Category: Gong, X]]	+	[[Category: Du M]]
-	[[Category: Lu, P]]	+	[[Category: Gong X]]
-	[[Category: Ma, D]]	+	[[Category: Lu P]]
-	[[Category: Shi, Y]]	+	[[Category: Ma D]]
-	[[Category: Yan, C]]	+	[[Category: Shi Y]]
-	~~[[Category: Alpha helical membrane protein]]~~	+	[[Category: Yan C]]
-	~~[[Category: Ascorbate-dependent oxidoreductase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 08:28, 5 August 2016

OCA — Fri, 05 Aug 2016 08:28:57 GMT

←Older revision		Revision as of 08:28, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soaked in 1 M L-ascorbate for 10 minutes==		==Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soaked in 1 M L-ascorbate for 10 minutes==
	<StructureSection load='4o79' size='340' side='right' caption='[[4o79]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4o79' size='340' side='right' caption='[[4o79]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CYB561B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CYB561B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ascorbate_ferrireductase_(transmembrane) Ascorbate ferrireductase (transmembrane)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.16.5.1 1.16.5.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ascorbate_ferrireductase_(transmembrane) Ascorbate ferrireductase (transmembrane)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.16.5.1 1.16.5.1] </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=4o79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o79 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o79 RCSB], [http://www.ebi.ac.uk/pdbsum/4o79 PDBsum]</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=4o79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o79 OCA], [http://pdbe.org/4o79 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4o79 RCSB], [http://www.ebi.ac.uk/pdbsum/4o79 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4o79 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 4o79" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 00:44, 25 December 2014

OCA — Thu, 25 Dec 2014 00:44:59 GMT

←Older revision		Revision as of 00:44, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4o79\| PDB=4o79 \| SCENE= }}~~	+	==Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soaked in 1 M L-ascorbate for 10 minutes==
-	===Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soaked in 1 M L-ascorbate for 10 minutes===	+	<StructureSection load='4o79' size='340' side='right' caption='[[4o79]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24449903}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4o79]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O79 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O79 FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASC:ASCORBIC+ACID'>ASC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4o6y\|4o6y]], [[4o7g\|4o7g]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CYB561B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ascorbate_ferrireductase_(transmembrane) Ascorbate ferrireductase (transmembrane)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.16.5.1 1.16.5.1] </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=4o79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o79 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o79 RCSB], [http://www.ebi.ac.uk/pdbsum/4o79 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/ACFR2_ARATH ACFR2_ARATH]] Two-heme-containing cytochrome. Catalyzes ascorbate-dependent trans-membrane ferric-chelate reduction (By similarity).		[[http://www.uniprot.org/uniprot/ACFR2_ARATH ACFR2_ARATH]] Two-heme-containing cytochrome. Catalyzes ascorbate-dependent trans-membrane ferric-chelate reduction (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Vitamin C, also known as ascorbate, is required in numerous essential metabolic reactions in eukaryotes. The eukaryotic ascorbate-dependent oxidoreductase cytochrome b561 (Cyt b561), a family of highly conserved transmembrane enzymes, plays an important role in ascorbate recycling and iron absorption. Although Cyt b561 was identified four decades ago, its atomic structure and functional mechanism remain largely unknown. Here, we report the high-resolution crystal structures of cytochrome b561 from Arabidopsis thaliana in both substrate-free and substrate-bound states. Cyt b561 forms a homodimer, with each protomer consisting of six transmembrane helices and two heme groups. The negatively charged substrate ascorbate, or monodehydroascorbate, is enclosed in a positively charged pocket on either side of the membrane. Two highly conserved amino acids, Lys81 and His106, play an essential role in substrate recognition and catalysis. Our structural and biochemical analyses allow the proposition of a general electron transfer mechanism for members of the Cyt b561 family.

-	~~==About this~~ Structure==	+	Structure and mechanism of a eukaryotic transmembrane ascorbate-dependent oxidoreductase.,Lu P, Ma D, Yan C, Gong X, Du M, Shi Y Proc Natl Acad Sci U S A. 2014 Jan 21. PMID:24449903<ref>PMID:24449903</ref>
-	~~[[4o79]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4O79 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024449903</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Du, M.]]	+	== References ==
-	[[Category: Gong, X.]]	+	<references/>
-	[[Category: Lu, P.]]	+	__TOC__
-	[[Category: Ma, D.]]	+	</StructureSection>
-	[[Category: Shi, Y.]]	+	[[Category: Arath]]
-	[[Category: Yan, C.]]	+	[[Category: Du, M]]
		+	[[Category: Gong, X]]
		+	[[Category: Lu, P]]
		+	[[Category: Ma, D]]
		+	[[Category: Shi, Y]]
		+	[[Category: Yan, C]]
	[[Category: Alpha helical membrane protein]]		[[Category: Alpha helical membrane protein]]
	[[Category: Ascorbate-dependent oxidoreductase]]		[[Category: Ascorbate-dependent oxidoreductase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 11:23, 5 February 2014

OCA — Wed, 05 Feb 2014 11:23:37 GMT

←Older revision		Revision as of 11:23, 5 February 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4o79\| PDB=4o79 \| SCENE= }}
		+	===Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soaked in 1 M L-ascorbate for 10 minutes===
		+	{{ABSTRACT_PUBMED_24449903}}

-	~~The entry 4o79 is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/ACFR2_ARATH ACFR2_ARATH]] Two-heme-containing cytochrome. Catalyzes ascorbate-dependent trans-membrane ferric-chelate reduction (By similarity).

-	~~Authors~~: ~~Lu, P., Ma, D., Yan, C~~.~~, Gong, X~~.~~, Du, M~~.~~, Shi, Y~~.	+	==About this Structure==
		+	[[4o79]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O79 OCA].

-	~~Description~~: ~~Crystal Structure of Ascorbate-bound Cytochrome b561~~, ~~crystal soaked in 1~~ M L-~~ascorbate for 10 minutes~~	+	==Reference==
		+	<ref group="xtra">PMID:024449903</ref><references group="xtra"/><references/>
		+	[[Category: Du, M.]]
		+	[[Category: Gong, X.]]
		+	[[Category: Lu, P.]]
		+	[[Category: Ma, D.]]
		+	[[Category: Shi, Y.]]
		+	[[Category: Yan, C.]]
		+	[[Category: Alpha helical membrane protein]]
		+	[[Category: Ascorbate-dependent oxidoreductase]]
		+	[[Category: Oxidoreductase]]

OCA at 06:46, 22 January 2014

OCA — Wed, 22 Jan 2014 06:46:29 GMT

←Older revision		Revision as of 06:46, 22 January 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4o79 is ON HOLD	+	The entry 4o79 is ON HOLD until Paper Publication

	Authors: Lu, P., Ma, D., Yan, C., Gong, X., Du, M., Shi, Y.		Authors: Lu, P., Ma, D., Yan, C., Gong, X., Du, M., Shi, Y.

-	Description: Crystal Structure of Cytochrome b561 soaked in 1 M L-ascorbate for 10 minutes	+	Description: Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soaked in 1 M L-ascorbate for 10 minutes

OCA: Protected "4o79" [edit=sysop:move=sysop]

OCA — Wed, 08 Jan 2014 09:25:57 GMT

Protected "4o79" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:25, 8 January 2014

OCA: New page: '''Unreleased structure''' The entry 4o79 is ON HOLD Authors: Lu, P., Ma, D., Yan, C., Gong, X., Du, M., Shi, Y. Description: Crystal Structure of Cytochrome b561 soaked in 1 M L-ascor...

OCA — Wed, 08 Jan 2014 09:25:55 GMT

New page: '''Unreleased structure''' The entry 4o79 is ON HOLD Authors: Lu, P., Ma, D., Yan, C., Gong, X., Du, M., Shi, Y. Description: Crystal Structure of Cytochrome b561 soaked in 1 M L-ascor...

New page

'''Unreleased structure'''

The entry 4o79 is ON HOLD

Authors: Lu, P., Ma, D., Yan, C., Gong, X., Du, M., Shi, Y.

Description: Crystal Structure of Cytochrome b561 soaked in 1 M L-ascorbate for 10 minutes