7d7q - Revision history

OCA at 16:27, 29 November 2023

OCA — Wed, 29 Nov 2023 16:27:59 GMT

←Older revision		Revision as of 16:27, 29 November 2023
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	<StructureSection load='7d7q' size='340' side='right'caption='[[7d7q]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='7d7q' size='340' side='right'caption='[[7d7q]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7d7q]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Proterospongia_sp._atcc_50818 Proterospongia sp. atcc 50818~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D7Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7D7Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7d7q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salpingoeca_rosetta Salpingoeca rosetta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D7Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D7Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=OLC:(2R)~~-2,3~~-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=RET:RETINAL'>RET</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]] 3.5Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[7cj3\|7cj3]], [[7d7p\|7d7p]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">PTSG_02023 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=946362 Proterospongia sp. ATCC 50818])~~</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=7d7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d7q OCA], [https://pdbe.org/7d7q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d7q RCSB], [https://www.ebi.ac.uk/pdbsum/7d7q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d7q ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=7d7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d7q OCA], [~~http~~://pdbe.org/7d7q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7d7q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7d7q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7d7q ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F2TZN0_SALR5 F2TZN0_SALR5]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7d7q" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7d7q" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Proterospongia sp. atcc 50818~~]]	+	[[Category: Salpingoeca rosetta]]
-	[[Category: Ikuta, T]]	+	[[Category: Ikuta T]]
-	[[Category: Nureki, O]]	+	[[Category: Nureki O]]
-	[[Category: Shihoya, W]]	+	[[Category: Shihoya W]]
-	[[Category: Yamashita, K]]	+	[[Category: Yamashita K]]
-	~~[[Category: Eight-transmembrane]]~~	+
-	~~[[Category: Light-dependent phosphodiesterase]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Microbial rhodopsin~~]]	+

OCA at 07:17, 25 November 2020

OCA — Wed, 25 Nov 2020 07:17:20 GMT

←Older revision		Revision as of 07:17, 25 November 2020
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	==Crystal structure of the transmembrane domain and linker region of Salpingoeca rosetta rhodopsin phosphodiesterase==		==Crystal structure of the transmembrane domain and linker region of Salpingoeca rosetta rhodopsin phosphodiesterase==
-	<StructureSection load='7d7q' size='340' side='right'caption='[[7d7q]]' scene=''>	+	<StructureSection load='7d7q' size='340' side='right'caption='[[7d7q]], [[Resolution\|resolution]] 3.50Å' 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=7D7Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7D7Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7d7q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Proterospongia_sp._atcc_50818 Proterospongia sp. atcc 50818]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D7Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7D7Q FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7d7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d7q OCA], [http://pdbe.org/7d7q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7d7q RCSB], [http://www.ebi.ac.uk/pdbsum/7d7q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7d7q 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=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7cj3\|7cj3]], [[7d7p\|7d7p]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PTSG_02023 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=946362 Proterospongia sp. ATCC 50818])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7d7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d7q OCA], [http://pdbe.org/7d7q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7d7q RCSB], [http://www.ebi.ac.uk/pdbsum/7d7q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7d7q ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Rhodopsin phosphodiesterase (Rh-PDE) is an enzyme rhodopsin belonging to a recently discovered class of microbial rhodopsins with light-dependent enzymatic activity. Rh-PDE consists of the N-terminal rhodopsin domain and C-terminal phosphodiesterase (PDE) domain, connected by 76-residue linker, and hydrolyzes both cAMP and cGMP in a light-dependent manner. Thus, Rh-PDE has potential for the optogenetic manipulation of cyclic nucleotide concentrations, as a complementary tool to rhodopsin guanylyl cyclase and photosensitive adenylyl cyclase. Here we present structural and functional analyses of the Rh-PDE derived from Salpingoeca rosetta. The crystal structure of the rhodopsin domain at 2.6 A resolution revealed a new topology of rhodopsins, with 8 TMs including the N-terminal extra TM, TM0. Mutational analyses demonstrated that TM0 plays a crucial role in the enzymatic photoactivity. We further solved the crystal structures of the rhodopsin domain (3.5 A) and PDE domain (2.1 A) with their connecting linkers, which showed a rough sketch of the full-length Rh-PDE. Integrating these structures, we proposed a model of full-length Rh-PDE, based on the HS-AFM observations and computational modeling of the linker region. These findings provide insight into the photoactivation mechanisms of other 8-TM enzyme rhodopsins and expand the definition of rhodopsins.
		+
		+	Structural insights into the mechanism of rhodopsin phosphodiesterase.,Ikuta T, Shihoya W, Sugiura M, Yoshida K, Watari M, Tokano T, Yamashita K, Katayama K, Tsunoda SP, Uchihashi T, Kandori H, Nureki O Nat Commun. 2020 Nov 5;11(1):5605. doi: 10.1038/s41467-020-19376-7. PMID:33154353<ref>PMID:33154353</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7d7q" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ikuta T]]	+	[[Category: Proterospongia sp. atcc 50818]]
-	[[Category: Nureki O]]	+	[[Category: Ikuta, T]]
-	[[Category: Shihoya W]]	+	[[Category: Nureki, O]]
-	[[Category: Yamashita K]]	+	[[Category: Shihoya, W]]
		+	[[Category: Yamashita, K]]
		+	[[Category: Eight-transmembrane]]
		+	[[Category: Light-dependent phosphodiesterase]]
		+	[[Category: Membrane protein]]
		+	[[Category: Microbial rhodopsin]]

OCA at 09:41, 18 November 2020

OCA — Wed, 18 Nov 2020 09:41:29 GMT

←Older revision		Revision as of 09:41, 18 November 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7d7q is ~~ON HOLD~~	+	==Crystal structure of the transmembrane domain and linker region of Salpingoeca rosetta rhodopsin phosphodiesterase==
-		+	<StructureSection load='7d7q' size='340' side='right'caption='[[7d7q]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D7Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7D7Q FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7d7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d7q OCA], [http://pdbe.org/7d7q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7d7q RCSB], [http://www.ebi.ac.uk/pdbsum/7d7q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7d7q ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ikuta T]]
		+	[[Category: Nureki O]]
		+	[[Category: Shihoya W]]
		+	[[Category: Yamashita K]]

OCA: Protected "7d7q" [edit=sysop:move=sysop]

OCA — Wed, 14 Oct 2020 04:12:11 GMT

Protected "7d7q" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:12, 14 October 2020

OCA: New page: '''Unreleased structure''' The entry 7d7q is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 14 Oct 2020 04:12:10 GMT

New page: '''Unreleased structure''' The entry 7d7q is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7d7q is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]