5yqz - Revision history

OCA at 08:35, 22 November 2023

OCA — Wed, 22 Nov 2023 08:35:41 GMT

←Older revision		Revision as of 08:35, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5yqz' size='340' side='right'caption='[[5yqz]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='5yqz' size='340' side='right'caption='[[5yqz]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yqz]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YQZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YQZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yqz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4] 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=5YQZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YQZ 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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~GCGR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17]~~ </~~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=5yqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yqz OCA], [https://pdbe.org/5yqz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yqz RCSB], [https://www.ebi.ac.uk/pdbsum/5yqz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yqz 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=5yqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yqz OCA], [~~http~~://pdbe.org/5yqz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yqz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yqz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yqz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GLR_HUMAN GLR_HUMAN]] This is a receptor for glucagon which plays a central role in regulating the level of blood glucose by controlling the rate of hepatic glucose production and insulin secretion. The activity of this receptor is mediated by G proteins which activate adenylyl cyclase and also a phosphatidylinositol-calcium second messenger system.	+	[https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref> [https://www.uniprot.org/uniprot/GLR_HUMAN GLR_HUMAN] This is a receptor for glucagon which plays a central role in regulating the level of blood glucose by controlling the rate of hepatic glucose production and insulin secretion. The activity of this receptor is mediated by G proteins which activate adenylyl cyclase and also a phosphatidylinositol-calcium second messenger system.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	==See Also==		==See Also==
	*[[Glucagon\|Glucagon]]		*[[Glucagon\|Glucagon]]
		+	*[[Glucagon receptor\|Glucagon receptor]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Escherichia virus T4]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Cai X]]
-	[[Category: Cai, X]]	+	[[Category: Can C]]
-	[[Category: Can, C]]	+	[[Category: Dai A]]
-	[[Category: Dai, A]]	+	[[Category: Ernst O]]
-	~~[[Category: EPS, N VAN~~]]	+	[[Category: Frederiksen K]]
-	[[Category: Ernst, O]]	+	[[Category: Hanson M]]
-	[[Category: Frederiksen, K]]	+	[[Category: He L]]
-	[[Category: Hanson, M]]	+	[[Category: Jiang H]]
-	[[Category: He, L]]	+	[[Category: Lau J]]
-	[[Category: Jiang, H]]	+	[[Category: Qiao A]]
-	[[Category: Lau, J]]	+	[[Category: Seedtz-Runge S]]
-	[[Category: Qiao, A]]	+	[[Category: Stevens R]]
-	[[Category: Seedtz-Runge, S]]	+	[[Category: VAN EPS N]]
-	[[Category: Stevens, R]]	+	[[Category: Wang M]]
-	[[Category: Wang, M]]	+	[[Category: Wu B]]
-	[[Category: Wu, B]]	+	[[Category: Yang D]]
-	[[Category: Yang, D]]	+	[[Category: Yang H]]
-	[[Category: Yang, H]]	+	[[Category: Yang L]]
-	[[Category: Yang, L]]	+	[[Category: Yi C]]
-	[[Category: Yi, C]]	+	[[Category: Zhang H]]
-	[[Category: Zhang, H]]	+	[[Category: Zhao Q]]
-	[[Category: Zhao, Q]]	+
-	~~[[Category: 7tm domain]]~~	+
-	~~[[Category: Class b]]~~	+
-	~~[[Category: Human gcgr receptor]]~~	+
-	~~[[Category: Lcp]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Signaling protein-hydrolase complex]]~~	+
-	~~[[Category: Xfel~~]]	+

OCA at 09:25, 21 October 2020

OCA — Wed, 21 Oct 2020 09:25:52 GMT

←Older revision		Revision as of 09:25, 21 October 2020
Line 1:		Line 1:

	==Structure of the glucagon receptor in complex with a glucagon analogue==		==Structure of the glucagon receptor in complex with a glucagon analogue==
-	<StructureSection load='5yqz' size='340' side='right' caption='[[5yqz]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='5yqz' size='340' side='right'caption='[[5yqz]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yqz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YQZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YQZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yqz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YQZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YQZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'~~>~~NAG</scene>,~~ <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GCGR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=5yqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yqz OCA], [http://pdbe.org/5yqz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yqz RCSB], [http://www.ebi.ac.uk/pdbsum/5yqz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yqz 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=5yqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yqz OCA], [http://pdbe.org/5yqz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yqz RCSB], [http://www.ebi.ac.uk/pdbsum/5yqz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yqz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5yqz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5yqz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glucagon\|Glucagon]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Cai, X]]		[[Category: Cai, X]]

OCA at 06:58, 17 January 2018

OCA — Wed, 17 Jan 2018 06:58:50 GMT

←Older revision		Revision as of 06:58, 17 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yqz is ~~ON HOLD until Paper~~ Publication	+	==Structure of the glucagon receptor in complex with a glucagon analogue==
		+	<StructureSection load='5yqz' size='340' side='right' caption='[[5yqz]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yqz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YQZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YQZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=5yqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yqz OCA], [http://pdbe.org/5yqz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yqz RCSB], [http://www.ebi.ac.uk/pdbsum/5yqz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yqz ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GLR_HUMAN GLR_HUMAN]] This is a receptor for glucagon which plays a central role in regulating the level of blood glucose by controlling the rate of hepatic glucose production and insulin secretion. The activity of this receptor is mediated by G proteins which activate adenylyl cyclase and also a phosphatidylinositol-calcium second messenger system.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Class B G-protein-coupled receptors (GPCRs), which consist of an extracellular domain (ECD) and a transmembrane domain (TMD), respond to secretin peptides to play a key part in hormonal homeostasis, and are important therapeutic targets for a variety of diseases. Previous work has suggested that peptide ligands bind to class B GPCRs according to a two-domain binding model, in which the C-terminal region of the peptide targets the ECD and the N-terminal region of the peptide binds to the TMD binding pocket. Recently, three structures of class B GPCRs in complex with peptide ligands have been solved. These structures provide essential insights into peptide ligand recognition by class B GPCRs. However, owing to resolution limitations, the specific molecular interactions for peptide binding to class B GPCRs remain ambiguous. Moreover, these previously solved structures have different ECD conformations relative to the TMD, which introduces questions regarding inter-domain conformational flexibility and the changes required for receptor activation. Here we report the 3.0 A-resolution crystal structure of the full-length human glucagon receptor (GCGR) in complex with a glucagon analogue and partial agonist, NNC1702. This structure provides molecular details of the interactions between GCGR and the peptide ligand. It reveals a marked change in the relative orientation between the ECD and TMD of GCGR compared to the previously solved structure of the inactive GCGR-NNC0640-mAb1 complex. Notably, the stalk region and the first extracellular loop undergo major conformational changes in secondary structure during peptide binding, forming key interactions with the peptide. We further propose a dual-binding-site trigger model for GCGR activation-which requires conformational changes of the stalk, first extracellular loop and TMD-that extends our understanding of the previously established two-domain peptide-binding model of class B GPCRs.

-	~~Authors~~:	+	Structure of the glucagon receptor in complex with a glucagon analogue.,Zhang H, Qiao A, Yang L, Van Eps N, Frederiksen KS, Yang D, Dai A, Cai X, Zhang H, Yi C, Cao C, He L, Yang H, Lau J, Ernst OP, Hanson MA, Stevens RC, Wang MW, Reedtz-Runge S, Jiang H, Zhao Q, Wu B Nature. 2018 Jan 3;553(7686):106-110. doi: 10.1038/nature25153. PMID:29300013<ref>PMID:29300013</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5yqz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lysozyme]]
		+	[[Category: Cai, X]]
		+	[[Category: Can, C]]
		+	[[Category: Dai, A]]
		+	[[Category: EPS, N VAN]]
		+	[[Category: Ernst, O]]
		+	[[Category: Frederiksen, K]]
		+	[[Category: Hanson, M]]
		+	[[Category: He, L]]
		+	[[Category: Jiang, H]]
		+	[[Category: Lau, J]]
		+	[[Category: Qiao, A]]
		+	[[Category: Seedtz-Runge, S]]
		+	[[Category: Stevens, R]]
		+	[[Category: Wang, M]]
		+	[[Category: Wu, B]]
		+	[[Category: Yang, D]]
		+	[[Category: Yang, H]]
		+	[[Category: Yang, L]]
		+	[[Category: Yi, C]]
		+	[[Category: Zhang, H]]
		+	[[Category: Zhao, Q]]
		+	[[Category: 7tm domain]]
		+	[[Category: Class b]]
		+	[[Category: Human gcgr receptor]]
		+	[[Category: Lcp]]
		+	[[Category: Membrane]]
		+	[[Category: Signaling protein]]
		+	[[Category: Signaling protein-hydrolase complex]]
		+	[[Category: Xfel]]

OCA at 05:46, 13 December 2017

OCA — Wed, 13 Dec 2017 05:46:10 GMT

←Older revision		Revision as of 05:46, 13 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yqz is ON HOLD	+	The entry 5yqz is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5yqz" [edit=sysop:move=sysop]

OCA — Wed, 15 Nov 2017 06:17:01 GMT

Protected "5yqz" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:17, 15 November 2017

OCA: New page: '''Unreleased structure''' The entry 5yqz is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 15 Nov 2017 06:17:00 GMT

New page: '''Unreleased structure''' The entry 5yqz is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5yqz is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]