5gkz - Revision history

OCA at 10:16, 27 March 2024

OCA — Wed, 27 Mar 2024 10:16:19 GMT

←Older revision		Revision as of 10:16, 27 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/RYR1_RABIT RYR1_RABIT] Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering muscle contraction following depolarization of T-tubules. Repeated very high-level exercise increases the open probability of the channel and leads to Ca(2+) leaking into the cytoplasm. Can also mediate the release of Ca(2+) from intracellular stores in neurons, and may thereby promote prolonged Ca(2+) signaling in the brain. Required for normal embryonic development of muscle fibers and skeletal muscle. Required for normal heart morphogenesis, skin development and ossification during embryogenesis (By similarity).<ref>PMID:10388749</ref> <ref>PMID:22036948</ref>		[https://www.uniprot.org/uniprot/RYR1_RABIT RYR1_RABIT] Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering muscle contraction following depolarization of T-tubules. Repeated very high-level exercise increases the open probability of the channel and leads to Ca(2+) leaking into the cytoplasm. Can also mediate the release of Ca(2+) from intracellular stores in neurons, and may thereby promote prolonged Ca(2+) signaling in the brain. Required for normal embryonic development of muscle fibers and skeletal muscle. Required for normal heart morphogenesis, skin development and ossification during embryogenesis (By similarity).<ref>PMID:10388749</ref> <ref>PMID:22036948</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The ryanodine receptors (RyRs) are intracellular calcium channels responsible for rapid release of Ca(2+) from the sarcoplasmic/endoplasmic reticulum (SR/ER) to the cytoplasm, which is essential for the excitation-contraction (E-C) coupling of cardiac and skeletal muscles. The near-atomic resolution structure of closed RyR1 revealed the molecular details of this colossal channel, while the long-range allosteric gating mechanism awaits elucidation. Here, we report the cryo-EM structures of rabbit RyR1 in three closed conformations at about 4 A resolution and an open state at 5.7 A. Comparison of the closed RyR1 structures shows a breathing motion of the cytoplasmic platform, while the channel domain and its contiguous Central domain remain nearly unchanged. Comparison of the open and closed structures shows a dilation of the S6 tetrahelical bundle at the cytoplasmic gate that leads to channel opening. During the pore opening, the cytoplasmic "O-ring" motif of the channel domain and the U-motif of the Central domain exhibit coupled motion, while the Central domain undergoes domain-wise displacement. These structural analyses provide important insight into the E-C coupling in skeletal muscles and identify the Central domain as the transducer that couples the conformational changes of the cytoplasmic platform to the gating of the central pore.
-
-	The Central domain of RyR1 is the transducer for long-range allosteric gating of channel opening.,Bai XC, Yan Z, Wu J, Li Z, Yan N Cell Res. 2016 Sep;26(9):995-1006. doi: 10.1038/cr.2016.89. Epub 2016 Jul 29. PMID:27468892<ref>PMID:27468892</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5gkz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:34, 2 August 2023

OCA — Wed, 02 Aug 2023 11:34:49 GMT

←Older revision		Revision as of 11:34, 2 August 2023
Line 3:		Line 3:
	<SX load='5gkz' size='340' side='right' viewer='molstar' caption='[[5gkz]], [[Resolution\|resolution]] 4.00Å' scene=''>		<SX load='5gkz' size='340' side='right' viewer='molstar' caption='[[5gkz]], [[Resolution\|resolution]] 4.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gkz]] is a 8 chain structure with sequence from [~~http://en.wikipedia.org/wiki/European_rabbit European rabbit] and [http~~://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5GKZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gkz]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GKZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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">Electron Microscopy, [[Resolution\|Resolution]] 4Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3j8h\|3j8h]]~~, [[~~5gky~~\|~~5gky]], [[5gl0\|5gl0]], [[5gl1\|5gl1~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>FKBP12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9986 European rabbit])</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=5gkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkz OCA], [https://pdbe.org/5gkz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gkz RCSB], [https://www.ebi.ac.uk/pdbsum/5gkz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkz ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8]~~ </~~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=5gkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkz OCA], [~~http~~://pdbe.org/5gkz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gkz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gkz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RYR1_RABIT RYR1_RABIT]] Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering muscle contraction following depolarization of T-tubules. Repeated very high-level exercise increases the open probability of the channel and leads to Ca(2+) leaking into the cytoplasm. Can also mediate the release of Ca(2+) from intracellular stores in neurons, and may thereby promote prolonged Ca(2+) signaling in the brain. Required for normal embryonic development of muscle fibers and skeletal muscle. Required for normal heart morphogenesis, skin development and ossification during embryogenesis (By similarity).<ref>PMID:10388749</ref> <ref>PMID:22036948</ref> [[http://www.uniprot.org/uniprot/FKB1A_RABIT FKB1A_RABIT]] Keeps in an inactive conformation TGFBR1, the TGF-beta type I serine/threonine kinase receptor, preventing TGF-beta receptor activation in absence of ligand. Recruites SMAD7 to ACVR1B which prevents the association of SMAD2 and SMAD3 with the activin receptor complex, thereby blocking the activin signal. May modulate the RYR1 calcium channel activity. PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity).	+	[https://www.uniprot.org/uniprot/RYR1_RABIT RYR1_RABIT] Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering muscle contraction following depolarization of T-tubules. Repeated very high-level exercise increases the open probability of the channel and leads to Ca(2+) leaking into the cytoplasm. Can also mediate the release of Ca(2+) from intracellular stores in neurons, and may thereby promote prolonged Ca(2+) signaling in the brain. Required for normal embryonic development of muscle fibers and skeletal muscle. Required for normal heart morphogenesis, skin development and ossification during embryogenesis (By similarity).<ref>PMID:10388749</ref> <ref>PMID:22036948</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5gkz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5gkz" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ryanodine receptor 3D structures\|Ryanodine receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: European rabbit]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Oryctolagus cuniculus]]		[[Category: Oryctolagus cuniculus]]
-	~~[[Category: Peptidylprolyl isomerase]]~~	+	[[Category: Bai XC]]
-	[[Category: Bai~~, X C~~]]	+	[[Category: Wu JP]]
-	[[Category: Wu~~, J P~~]]	+	[[Category: Yan N]]
-	[[Category: Yan, N]]	+	[[Category: Yan Z]]
-	[[Category: Yan, Z]]	+
-	~~[[Category: Channel]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Transport protein-isomerase complex~~]]	+

OCA at 20:05, 10 April 2020

OCA — Fri, 10 Apr 2020 20:05:59 GMT

←Older revision		Revision as of 20:05, 10 April 2020
Line 3:		Line 3:
	<SX load='5gkz' size='340' side='right' viewer='molstar' caption='[[5gkz]], [[Resolution\|resolution]] 4.00Å' scene=''>		<SX load='5gkz' size='340' side='right' viewer='molstar' caption='[[5gkz]], [[Resolution\|resolution]] 4.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gkz]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GKZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gkz]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GKZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3j8h\|3j8h]], [[5gky\|5gky]], [[5gl0\|5gl0]], [[5gl1\|5gl1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3j8h\|3j8h]], [[5gky\|5gky]], [[5gl0\|5gl0]], [[5gl1\|5gl1]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FKBP12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9986 European rabbit])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FKBP12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9986 European rabbit])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </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=5gkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkz OCA], [http://pdbe.org/5gkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gkz RCSB], [http://www.ebi.ac.uk/pdbsum/5gkz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkz 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=5gkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkz OCA], [http://pdbe.org/5gkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gkz RCSB], [http://www.ebi.ac.uk/pdbsum/5gkz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 18:28, 6 March 2020

OCA — Fri, 06 Mar 2020 18:28:25 GMT

←Older revision		Revision as of 18:28, 6 March 2020
Line 1:		Line 1:

	==Structure of RyR1 in a closed state (C3 conformer)==		==Structure of RyR1 in a closed state (C3 conformer)==
-	<~~StructureSection~~ load='5gkz' size='340' side='right'caption='[[5gkz]], [[Resolution\|resolution]] 4.00Å' scene=''>	+	<SX load='5gkz' size='340' side='right' viewer='molstar' caption='[[5gkz]], [[Resolution\|resolution]] 4.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5gkz]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GKZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5gkz]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GKZ FirstGlance]. <br>
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[Ryanodine receptor\|Ryanodine receptor]]	+	*[[Ryanodine receptor 3D structures\|Ryanodine receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: European rabbit]]		[[Category: European rabbit]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 06:20, 16 October 2019

OCA — Wed, 16 Oct 2019 06:20:21 GMT

←Older revision		Revision as of 06:20, 16 October 2019
Line 1:		Line 1:
-	~~{{Large structure}}~~	+
	==Structure of RyR1 in a closed state (C3 conformer)==		==Structure of RyR1 in a closed state (C3 conformer)==
-	<StructureSection load='5gkz' size='340' side='right' caption='[[5gkz]], [[Resolution\|resolution]] 4.00Å' scene=''>	+	<StructureSection load='5gkz' size='340' side='right'caption='[[5gkz]], [[Resolution\|resolution]] 4.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gkz]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GKZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gkz]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GKZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3j8h\|3j8h]], [[5gky\|5gky]], [[5gl0\|5gl0]], [[5gl1\|5gl1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3j8h\|3j8h]], [[5gky\|5gky]], [[5gl0\|5gl0]], [[5gl1\|5gl1]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FKBP12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9986 European rabbit])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </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=5gkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkz OCA], [http://pdbe.org/5gkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gkz RCSB], [http://www.ebi.ac.uk/pdbsum/5gkz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkz 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=5gkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkz OCA], [http://pdbe.org/5gkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gkz RCSB], [http://www.ebi.ac.uk/pdbsum/5gkz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkz ProSAT]</span></td></tr>
	</table>		</table>
-	{{Large structure}}
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RYR1_RABIT RYR1_RABIT]] Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering muscle contraction following depolarization of T-tubules. Repeated very high-level exercise increases the open probability of the channel and leads to Ca(2+) leaking into the cytoplasm. Can also mediate the release of Ca(2+) from intracellular stores in neurons, and may thereby promote prolonged Ca(2+) signaling in the brain. Required for normal embryonic development of muscle fibers and skeletal muscle. Required for normal heart morphogenesis, skin development and ossification during embryogenesis (By similarity).<ref>PMID:10388749</ref> <ref>PMID:22036948</ref> [[http://www.uniprot.org/uniprot/FKB1A_RABIT FKB1A_RABIT]] Keeps in an inactive conformation TGFBR1, the TGF-beta type I serine/threonine kinase receptor, preventing TGF-beta receptor activation in absence of ligand. Recruites SMAD7 to ACVR1B which prevents the association of SMAD2 and SMAD3 with the activin receptor complex, thereby blocking the activin signal. May modulate the RYR1 calcium channel activity. PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity).		[[http://www.uniprot.org/uniprot/RYR1_RABIT RYR1_RABIT]] Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering muscle contraction following depolarization of T-tubules. Repeated very high-level exercise increases the open probability of the channel and leads to Ca(2+) leaking into the cytoplasm. Can also mediate the release of Ca(2+) from intracellular stores in neurons, and may thereby promote prolonged Ca(2+) signaling in the brain. Required for normal embryonic development of muscle fibers and skeletal muscle. Required for normal heart morphogenesis, skin development and ossification during embryogenesis (By similarity).<ref>PMID:10388749</ref> <ref>PMID:22036948</ref> [[http://www.uniprot.org/uniprot/FKB1A_RABIT FKB1A_RABIT]] Keeps in an inactive conformation TGFBR1, the TGF-beta type I serine/threonine kinase receptor, preventing TGF-beta receptor activation in absence of ligand. Recruites SMAD7 to ACVR1B which prevents the association of SMAD2 and SMAD3 with the activin receptor complex, thereby blocking the activin signal. May modulate the RYR1 calcium channel activity. PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity).
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5gkz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5gkz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ryanodine receptor\|Ryanodine receptor]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: European rabbit]]
		+	[[Category: Large Structures]]
	[[Category: Oryctolagus cuniculus]]		[[Category: Oryctolagus cuniculus]]
	[[Category: Peptidylprolyl isomerase]]		[[Category: Peptidylprolyl isomerase]]

OCA at 06:56, 10 September 2016

OCA — Sat, 10 Sep 2016 06:56:38 GMT

←Older revision		Revision as of 06:56, 10 September 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	{{Large structure}}
		+	==Structure of RyR1 in a closed state (C3 conformer)==
		+	<StructureSection load='5gkz' size='340' side='right' caption='[[5gkz]], [[Resolution\|resolution]] 4.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5gkz]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GKZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3j8h\|3j8h]], [[5gky\|5gky]], [[5gl0\|5gl0]], [[5gl1\|5gl1]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </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=5gkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkz OCA], [http://pdbe.org/5gkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gkz RCSB], [http://www.ebi.ac.uk/pdbsum/5gkz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkz ProSAT]</span></td></tr>
		+	</table>
		+	{{Large structure}}
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RYR1_RABIT RYR1_RABIT]] Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering muscle contraction following depolarization of T-tubules. Repeated very high-level exercise increases the open probability of the channel and leads to Ca(2+) leaking into the cytoplasm. Can also mediate the release of Ca(2+) from intracellular stores in neurons, and may thereby promote prolonged Ca(2+) signaling in the brain. Required for normal embryonic development of muscle fibers and skeletal muscle. Required for normal heart morphogenesis, skin development and ossification during embryogenesis (By similarity).<ref>PMID:10388749</ref> <ref>PMID:22036948</ref> [[http://www.uniprot.org/uniprot/FKB1A_RABIT FKB1A_RABIT]] Keeps in an inactive conformation TGFBR1, the TGF-beta type I serine/threonine kinase receptor, preventing TGF-beta receptor activation in absence of ligand. Recruites SMAD7 to ACVR1B which prevents the association of SMAD2 and SMAD3 with the activin receptor complex, thereby blocking the activin signal. May modulate the RYR1 calcium channel activity. PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The ryanodine receptors (RyRs) are intracellular calcium channels responsible for rapid release of Ca(2+) from the sarcoplasmic/endoplasmic reticulum (SR/ER) to the cytoplasm, which is essential for the excitation-contraction (E-C) coupling of cardiac and skeletal muscles. The near-atomic resolution structure of closed RyR1 revealed the molecular details of this colossal channel, while the long-range allosteric gating mechanism awaits elucidation. Here, we report the cryo-EM structures of rabbit RyR1 in three closed conformations at about 4 A resolution and an open state at 5.7 A. Comparison of the closed RyR1 structures shows a breathing motion of the cytoplasmic platform, while the channel domain and its contiguous Central domain remain nearly unchanged. Comparison of the open and closed structures shows a dilation of the S6 tetrahelical bundle at the cytoplasmic gate that leads to channel opening. During the pore opening, the cytoplasmic "O-ring" motif of the channel domain and the U-motif of the Central domain exhibit coupled motion, while the Central domain undergoes domain-wise displacement. These structural analyses provide important insight into the E-C coupling in skeletal muscles and identify the Central domain as the transducer that couples the conformational changes of the cytoplasmic platform to the gating of the central pore.

-	The ~~entry 5gkz~~ is ~~ON HOLD~~	+	The Central domain of RyR1 is the transducer for long-range allosteric gating of channel opening.,Bai XC, Yan Z, Wu J, Li Z, Yan N Cell Res. 2016 Sep;26(9):995-1006. doi: 10.1038/cr.2016.89. Epub 2016 Jul 29. PMID:27468892<ref>PMID:27468892</ref>

-	~~Authors~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~:	+	<div class="pdbe-citations 5gkz" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Oryctolagus cuniculus]]
		+	[[Category: Peptidylprolyl isomerase]]
		+	[[Category: Bai, X C]]
		+	[[Category: Wu, J P]]
		+	[[Category: Yan, N]]
		+	[[Category: Yan, Z]]
		+	[[Category: Channel]]
		+	[[Category: Membrane protein]]
		+	[[Category: Transport protein-isomerase complex]]

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

OCA — Thu, 14 Jul 2016 06:39:05 GMT

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

←Older revision

Revision as of 06:39, 14 July 2016

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

OCA — Thu, 14 Jul 2016 06:39:03 GMT

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

New page

'''Unreleased structure'''

The entry 5gkz is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]