6me9 - Revision history

OCA at 06:29, 11 October 2023

2023-10-11T06:29:38Z

←Older revision		Revision as of 06:29, 11 October 2023
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	<StructureSection load='6me9' size='340' side='right'caption='[[6me9]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='6me9' size='340' side='right'caption='[[6me9]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6me9]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ME9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6ME9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6me9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum], [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ME9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ME9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JEV:N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide'>JEV</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]] 3.3Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTNR1B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JEV:N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide'>JEV</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~~://proteopedia.org/fgij/fg.htm?mol=6me9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6me9 OCA], [~~http~~://pdbe.org/6me9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6me9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6me9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6me9 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=6me9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6me9 OCA], [https://pdbe.org/6me9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6me9 RCSB], [https://www.ebi.ac.uk/pdbsum/6me9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6me9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX]] Electron-transport protein of unknown function.	+	[https://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX] Electron-transport protein of unknown function.[https://www.uniprot.org/uniprot/RUBR_CLOPA RUBR_CLOPA] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule.[https://www.uniprot.org/uniprot/MTR1B_HUMAN MTR1B_HUMAN] High affinity receptor for melatonin. Likely to mediate the reproductive and circadian actions of melatonin. The activity of this receptor is mediated by pertussis toxin sensitive G proteins that inhibit adenylate cyclase activity.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Clostridium pasteurianum]]
		+	[[Category: Escherichia coli]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Batyuk, A]]	+	[[Category: Batyuk A]]
-	[[Category: Cherezov, V]]	+	[[Category: Cherezov V]]
-	[[Category: Gati, C]]	+	[[Category: Gati C]]
-	[[Category: Grandner, J]]	+	[[Category: Grandner J]]
-	[[Category: Han~~, G W~~]]	+	[[Category: Han GW]]
-	[[Category: Hao, S]]	+	[[Category: Hao S]]
-	[[Category: Johansson~~, L C~~]]	+	[[Category: Johansson LC]]
-	[[Category: Katritch, V]]	+	[[Category: Katritch V]]
-	[[Category: Li, C]]	+	[[Category: Li C]]
-	[[Category: Liu, W]]	+	[[Category: Liu W]]
-	[[Category: McCorvy, J]]	+	[[Category: McCorvy J]]
-	[[Category: Olsen~~, R H.J~~]]	+	[[Category: Olsen RHJ]]
-	[[Category: Patel, N]]	+	[[Category: Patel N]]
-	[[Category: Roth~~, B L~~]]	+	[[Category: Roth BL]]
-	[[Category: Stauch, B]]	+	[[Category: Stauch B]]
-	[[Category: Tribo~~, A R~~]]	+	[[Category: Tribo AR]]
-	[[Category: Weierstall, U]]	+	[[Category: Weierstall U]]
-	[[Category: Zaare, S]]	+	[[Category: Zaare S]]
-	[[Category: Zatsepin~~, N A~~]]	+	[[Category: Zatsepin NA]]
-	[[Category: Zhu, L]]	+	[[Category: Zhu L]]
-	~~[[Category: Bril]]~~	+
-	~~[[Category: Circadian rhythm]]~~	+
-	~~[[Category: Gpcr]]~~	+
-	~~[[Category: Jetlag]]~~	+
-	~~[[Category: Lcp]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Ramelteon]]~~	+
-	~~[[Category: Rubredoxin]]~~	+
-	~~[[Category: Type 2 diabetes]]~~	+
-	~~[[Category: Xfel~~]]	+

OCA at 07:00, 29 April 2020

2020-04-29T07:00:11Z

←Older revision		Revision as of 07:00, 29 April 2020
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	<StructureSection load='6me9' size='340' side='right'caption='[[6me9]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='6me9' size='340' side='right'caption='[[6me9]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6me9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ME9 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ME9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6me9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ME9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ME9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JEV:N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide'>JEV</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=JEV:N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide'>JEV</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTNR1B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTNR1B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=6me9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6me9 OCA], [http://pdbe.org/6me9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6me9 RCSB], [http://www.ebi.ac.uk/pdbsum/6me9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6me9 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=6me9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6me9 OCA], [http://pdbe.org/6me9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6me9 RCSB], [http://www.ebi.ac.uk/pdbsum/6me9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6me9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 13:39, 10 May 2019

2019-05-10T13:39:48Z

←Older revision		Revision as of 13:39, 10 May 2019
Line 3:		Line 3:
	<StructureSection load='6me9' size='340' side='right'caption='[[6me9]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='6me9' size='340' side='right'caption='[[6me9]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6me9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ME9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ME9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6me9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ME9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ME9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JEV:N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide'>JEV</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"><scene name='pdbligand=JEV:N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide'>JEV</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MTNR1B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=6me9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6me9 OCA], [http://pdbe.org/6me9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6me9 RCSB], [http://www.ebi.ac.uk/pdbsum/6me9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6me9 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=6me9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6me9 OCA], [http://pdbe.org/6me9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6me9 RCSB], [http://www.ebi.ac.uk/pdbsum/6me9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6me9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX]] Electron-transport protein of unknown function.		[[http://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX]] Electron-transport protein of unknown function.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The human MT1 and MT2 melatonin receptors(1,2) are G-protein-coupled receptors (GPCRs) that help to regulate circadian rhythm and sleep patterns(3). Drug development efforts have targeted both receptors for the treatment of insomnia, circadian rhythm and mood disorders, and cancer(3), and MT2 has also been implicated in type 2 diabetes(4,5). Here we report X-ray free electron laser (XFEL) structures of the human MT2 receptor in complex with the agonists 2-phenylmelatonin (2-PMT) and ramelteon(6) at resolutions of 2.8 A and 3.3 A, respectively, along with two structures of function-related mutants: H208(5.46)A (superscripts represent the Ballesteros-Weinstein residue numbering nomenclature(7)) and N86(2.50)D, obtained in complex with 2-PMT. Comparison of the structures of MT2 with a published structure(8) of MT1 reveals that, despite conservation of the orthosteric ligand-binding site residues, there are notable conformational variations as well as differences in [(3)H]melatonin dissociation kinetics that provide insights into the selectivity between melatonin receptor subtypes. A membrane-buried lateral ligand entry channel is observed in both MT1 and MT2, but in addition the MT2 structures reveal a narrow opening towards the solvent in the extracellular part of the receptor. We provide functional and kinetic data that support a prominent role for intramembrane ligand entry in both receptors, and suggest that there might also be an extracellular entry path in MT2. Our findings contribute to a molecular understanding of melatonin receptor subtype selectivity and ligand access modes, which are essential for the design of highly selective melatonin tool compounds and therapeutic agents.
		+
		+	XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity.,Johansson LC, Stauch B, McCorvy JD, Han GW, Patel N, Huang XP, Batyuk A, Gati C, Slocum ST, Li C, Grandner JM, Hao S, Olsen RHJ, Tribo AR, Zaare S, Zhu L, Zatsepin NA, Weierstall U, Yous S, Stevens RC, Liu W, Roth BL, Katritch V, Cherezov V Nature. 2019 May;569(7755):289-292. doi: 10.1038/s41586-019-1144-0. Epub 2019 Apr, 24. PMID:31019305<ref>PMID:31019305</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6me9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Batyuk, A]]		[[Category: Batyuk, A]]

OCA at 06:57, 24 April 2019

2019-04-24T06:57:57Z

←Older revision		Revision as of 06:57, 24 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6me9 is ~~ON HOLD until Paper Publication~~	+	==XFEL crystal structure of human melatonin receptor MT2 in complex with ramelteon==
-		+	<StructureSection load='6me9' size='340' side='right'caption='[[6me9]], [[Resolution\|resolution]] 3.30Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6me9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ME9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ME9 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JEV:N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide'>JEV</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=6me9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6me9 OCA], [http://pdbe.org/6me9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6me9 RCSB], [http://www.ebi.ac.uk/pdbsum/6me9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6me9 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX]] Electron-transport protein of unknown function.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Batyuk, A]]
		+	[[Category: Cherezov, V]]
		+	[[Category: Gati, C]]
		+	[[Category: Grandner, J]]
		+	[[Category: Han, G W]]
		+	[[Category: Hao, S]]
		+	[[Category: Johansson, L C]]
		+	[[Category: Katritch, V]]
		+	[[Category: Li, C]]
		+	[[Category: Liu, W]]
		+	[[Category: McCorvy, J]]
		+	[[Category: Olsen, R H.J]]
		+	[[Category: Patel, N]]
		+	[[Category: Roth, B L]]
		+	[[Category: Stauch, B]]
		+	[[Category: Tribo, A R]]
		+	[[Category: Weierstall, U]]
		+	[[Category: Zaare, S]]
		+	[[Category: Zatsepin, N A]]
		+	[[Category: Zhu, L]]
		+	[[Category: Bril]]
		+	[[Category: Circadian rhythm]]
		+	[[Category: Gpcr]]
		+	[[Category: Jetlag]]
		+	[[Category: Lcp]]
		+	[[Category: Membrane protein]]
		+	[[Category: Ramelteon]]
		+	[[Category: Rubredoxin]]
		+	[[Category: Type 2 diabetes]]
		+	[[Category: Xfel]]

OCA at 18:24, 19 September 2018

2018-09-19T18:24:32Z

←Older revision		Revision as of 18:24, 19 September 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6me9 is ON HOLD	+	The entry 6me9 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6me9" [edit=sysop:move=sysop]

2018-09-12T06:18:15Z

Protected "6me9" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:18, 12 September 2018

OCA: New page: '''Unreleased structure''' The entry 6me9 is ON HOLD Authors: Description: Category: Unreleased Structures

2018-09-12T06:18:13Z

New page: '''Unreleased structure''' The entry 6me9 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6me9 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]