1s6i - Revision history

OCA at 09:07, 22 May 2024

OCA — Wed, 22 May 2024 09:07:26 GMT

←Older revision		Revision as of 09:07, 22 May 2024
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1s6i ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1s6i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Calcium-dependent protein kinases (CDPKs) are an extensive class of multidomain Ca(2+)-regulated enzymes from plants and protozoa. In vivo the so-called calmodulin-like domain (CLD) of CDPK binds intramolecularly to the junction domain (JD), which exhibits both kinase-inhibitory and CLD binding properties. Here we report the high resolution solution structure of the calcium-regulatory region from soybean CDPK-alpha determined in the presence of a peptide encompassing the JD. The structure of both lobes of CLD resembles that of related helix-loop-helix Ca(2+)-binding proteins. NMR chemical shift mapping studies demonstrate that the JD induces significant structural changes in isolated Ca(2+)-CLD, particularly the C-terminal domain, although a stable complex is not formed. A CLD solution structure calculated on the basis of NMR data and long range fluorescence resonance energy transfer distances reveals an activated state with both lobes positioned side by side, similar to calcineurin B rather than calmodulin, highlighting the possible pitfall of assigning function purely from sequence information.
		+
		+	Unexpected structure of the Ca2+-regulatory region from soybean calcium-dependent protein kinase-alpha.,Weljie AM, Vogel HJ J Biol Chem. 2004 Aug 20;279(34):35494-502. Epub 2004 May 20. PMID:15155727<ref>PMID:15155727</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1s6i" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Calcium-dependent protein kinase\|Calcium-dependent protein kinase]]		*[[Calcium-dependent protein kinase\|Calcium-dependent protein kinase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:29, 1 May 2024

OCA — Wed, 01 May 2024 08:29:27 GMT

←Older revision		Revision as of 08:29, 1 May 2024
Line 1:		Line 1:

	==Ca2+-regulatory region (CLD) from soybean calcium-dependent protein kinase-alpha (CDPK) in the presence of Ca2+ and the junction domain (JD)==		==Ca2+-regulatory region (CLD) from soybean calcium-dependent protein kinase-alpha (CDPK) in the presence of Ca2+ and the junction domain (JD)==
-	<StructureSection load='1s6i' size='340' side='right'caption='[[1s6i~~]], [[NMR_Ensembles_of_Models \| 15 NMR models~~]]' scene=''>	+	<StructureSection load='1s6i' size='340' side='right'caption='[[1s6i]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1s6i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Glycine_hispida~~ Glycine ~~hispida~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S6I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S6I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1s6i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S6I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S6I FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[1s6j\|1s6j]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">CDPK SK5 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])~~</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=1s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s6i OCA], [https://pdbe.org/1s6i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s6i RCSB], [https://www.ebi.ac.uk/pdbsum/1s6i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s6i 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=1s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s6i OCA], [https://pdbe.org/1s6i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s6i RCSB], [https://www.ebi.ac.uk/pdbsum/1s6i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s6i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CDPK_SOYBN CDPK_SOYBN]] May play a role in signal transduction pathways that involve calcium as a second messenger.	+	[https://www.uniprot.org/uniprot/CDPK_SOYBN CDPK_SOYBN] May play a role in signal transduction pathways that involve calcium as a second messenger.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1s6i ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1s6i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Calcium-dependent protein kinases (CDPKs) are an extensive class of multidomain Ca(2+)-regulated enzymes from plants and protozoa. In vivo the so-called calmodulin-like domain (CLD) of CDPK binds intramolecularly to the junction domain (JD), which exhibits both kinase-inhibitory and CLD binding properties. Here we report the high resolution solution structure of the calcium-regulatory region from soybean CDPK-alpha determined in the presence of a peptide encompassing the JD. The structure of both lobes of CLD resembles that of related helix-loop-helix Ca(2+)-binding proteins. NMR chemical shift mapping studies demonstrate that the JD induces significant structural changes in isolated Ca(2+)-CLD, particularly the C-terminal domain, although a stable complex is not formed. A CLD solution structure calculated on the basis of NMR data and long range fluorescence resonance energy transfer distances reveals an activated state with both lobes positioned side by side, similar to calcineurin B rather than calmodulin, highlighting the possible pitfall of assigning function purely from sequence information.
-
-	Unexpected structure of the Ca2+-regulatory region from soybean calcium-dependent protein kinase-alpha.,Weljie AM, Vogel HJ J Biol Chem. 2004 Aug 20;279(34):35494-502. Epub 2004 May 20. PMID:15155727<ref>PMID:15155727</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1s6i" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Calcium-dependent protein kinase\|Calcium-dependent protein kinase]]		*[[Calcium-dependent protein kinase\|Calcium-dependent protein kinase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Glycine ~~hispida~~]]	+	[[Category: Glycine max]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Vogel~~, H J~~]]	+	[[Category: Vogel HJ]]
-	[[Category: Weljie~~, A M]]~~	+	[[Category: Weljie AM]]
-	~~[[Category: Calcium-binding]]~~	+
-	~~[[Category: Calmodulin superfamily]]~~	+
-	~~[[Category: Ef-hand]]~~	+
-	~~[[Category: Helix-loop-helix]]~~	+
-	~~[[Category: Plant protein]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:33, 2 March 2022

OCA — Wed, 02 Mar 2022 06:33:57 GMT

←Older revision		Revision as of 06:33, 2 March 2022
Line 3:		Line 3:
	<StructureSection load='1s6i' size='340' side='right'caption='[[1s6i]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>		<StructureSection load='1s6i' size='340' side='right'caption='[[1s6i]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1s6i]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S6I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1S6I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1s6i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S6I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S6I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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;'>[[1s6j\|1s6j]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1s6j\|1s6j]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDPK SK5 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDPK SK5 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</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=1s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s6i OCA], [~~http~~://pdbe.org/1s6i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1s6i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1s6i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1s6i 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=1s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s6i OCA], [https://pdbe.org/1s6i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s6i RCSB], [https://www.ebi.ac.uk/pdbsum/1s6i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s6i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CDPK_SOYBN CDPK_SOYBN]] May play a role in signal transduction pathways that involve calcium as a second messenger.	+	[[https://www.uniprot.org/uniprot/CDPK_SOYBN CDPK_SOYBN]] May play a role in signal transduction pathways that involve calcium as a second messenger.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 13:41, 16 December 2020

OCA — Wed, 16 Dec 2020 13:41:47 GMT

←Older revision		Revision as of 13:41, 16 December 2020
Line 1:		Line 1:

	==Ca2+-regulatory region (CLD) from soybean calcium-dependent protein kinase-alpha (CDPK) in the presence of Ca2+ and the junction domain (JD)==		==Ca2+-regulatory region (CLD) from soybean calcium-dependent protein kinase-alpha (CDPK) in the presence of Ca2+ and the junction domain (JD)==
-	<StructureSection load='1s6i' size='340' side='right' caption='[[1s6i]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>	+	<StructureSection load='1s6i' size='340' side='right'caption='[[1s6i]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1s6i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S6I OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1S6I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1s6i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S6I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1S6I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s6j\|1s6j]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1s6j\|1s6j]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDPK SK5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDPK SK5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</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=1s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s6i OCA], [http://pdbe.org/1s6i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s6i RCSB], [http://www.ebi.ac.uk/pdbsum/1s6i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s6i 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=1s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s6i OCA], [http://pdbe.org/1s6i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s6i RCSB], [http://www.ebi.ac.uk/pdbsum/1s6i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s6i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Glycine hispida]]		[[Category: Glycine hispida]]
		+	[[Category: Large Structures]]
	[[Category: Vogel, H J]]		[[Category: Vogel, H J]]
	[[Category: Weljie, A M]]		[[Category: Weljie, A M]]

OCA at 06:40, 8 March 2018

OCA — Thu, 08 Mar 2018 06:40:34 GMT

←Older revision		Revision as of 06:40, 8 March 2018
Line 1:		Line 1:
		+
	==Ca2+-regulatory region (CLD) from soybean calcium-dependent protein kinase-alpha (CDPK) in the presence of Ca2+ and the junction domain (JD)==		==Ca2+-regulatory region (CLD) from soybean calcium-dependent protein kinase-alpha (CDPK) in the presence of Ca2+ and the junction domain (JD)==
	<StructureSection load='1s6i' size='340' side='right' caption='[[1s6i]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>		<StructureSection load='1s6i' size='340' side='right' caption='[[1s6i]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s6j\|1s6j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s6j\|1s6j]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDPK SK5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDPK SK5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</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=1s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s6i OCA], [http://pdbe.org/1s6i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s6i RCSB], [http://www.ebi.ac.uk/pdbsum/1s6i 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=1s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s6i OCA], [http://pdbe.org/1s6i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s6i RCSB], [http://www.ebi.ac.uk/pdbsum/1s6i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s6i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s6/1s6i_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s6/1s6i_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1s6i" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1s6i" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Calcium-dependent protein kinase\|Calcium-dependent protein kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:42, 9 February 2016

OCA — Tue, 09 Feb 2016 12:42:30 GMT

←Older revision		Revision as of 12:42, 9 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1s6i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1s6i" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1s6i" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Calcium-dependent protein kinase\|Calcium-dependent protein kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:21, 10 September 2015

OCA — Thu, 10 Sep 2015 22:21:22 GMT

←Older revision		Revision as of 22:21, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1s6i' size='340' side='right' caption='[[1s6i]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>		<StructureSection load='1s6i' size='340' side='right' caption='[[1s6i]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1s6i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Glycine_max~~ Glycine ~~max~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S6I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S6I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1s6i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S6I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S6I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s6j\|1s6j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s6j\|1s6j]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDPK SK5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine ~~max~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDPK SK5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</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=1s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s6i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s6i RCSB], [http://www.ebi.ac.uk/pdbsum/1s6i 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=1s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s6i OCA], [http://pdbe.org/1s6i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s6i RCSB], [http://www.ebi.ac.uk/pdbsum/1s6i PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 1s6i" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Glycine ~~max~~]]	+	[[Category: Glycine hispida]]
	[[Category: Vogel, H J]]		[[Category: Vogel, H J]]
	[[Category: Weljie, A M]]		[[Category: Weljie, A M]]

OCA at 06:53, 25 December 2014

OCA — Thu, 25 Dec 2014 06:53:37 GMT

←Older revision		Revision as of 06:53, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1s6i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S6I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S6I FirstGlance]. <br>		<table><tr><td colspan='2'>[[1s6i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S6I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S6I FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s6j\|1s6j]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s6j\|1s6j]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDPK SK5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine max])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDPK SK5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine max])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s6i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s6i RCSB], [http://www.ebi.ac.uk/pdbsum/1s6i 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=1s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s6i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s6i RCSB], [http://www.ebi.ac.uk/pdbsum/1s6i PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CDPK_SOYBN CDPK_SOYBN]] May play a role in signal transduction pathways that involve calcium as a second messenger.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Glycine max]]		[[Category: Glycine max]]
-	[[Category: Vogel, H J.]]	+	[[Category: Vogel, H J]]
-	[[Category: Weljie, A M.]]	+	[[Category: Weljie, A M]]
	[[Category: Calcium-binding]]		[[Category: Calcium-binding]]
	[[Category: Calmodulin superfamily]]		[[Category: Calmodulin superfamily]]

OCA at 13:53, 29 September 2014

OCA — Mon, 29 Sep 2014 13:53:47 GMT

←Older revision		Revision as of 13:53, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1s6i.~~png~~\|~~left~~\|200px]]	+	==Ca2+-regulatory region (CLD) from soybean calcium-dependent protein kinase-alpha (CDPK) in the presence of Ca2+ and the junction domain (JD)==
		+	<StructureSection load='1s6i' size='340' side='right' caption='[[1s6i]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1s6i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S6I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S6I FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s6j\|1s6j]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDPK SK5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine max])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1s6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s6i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s6i RCSB], [http://www.ebi.ac.uk/pdbsum/1s6i PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s6/1s6i_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Calcium-dependent protein kinases (CDPKs) are an extensive class of multidomain Ca(2+)-regulated enzymes from plants and protozoa. In vivo the so-called calmodulin-like domain (CLD) of CDPK binds intramolecularly to the junction domain (JD), which exhibits both kinase-inhibitory and CLD binding properties. Here we report the high resolution solution structure of the calcium-regulatory region from soybean CDPK-alpha determined in the presence of a peptide encompassing the JD. The structure of both lobes of CLD resembles that of related helix-loop-helix Ca(2+)-binding proteins. NMR chemical shift mapping studies demonstrate that the JD induces significant structural changes in isolated Ca(2+)-CLD, particularly the C-terminal domain, although a stable complex is not formed. A CLD solution structure calculated on the basis of NMR data and long range fluorescence resonance energy transfer distances reveals an activated state with both lobes positioned side by side, similar to calcineurin B rather than calmodulin, highlighting the possible pitfall of assigning function purely from sequence information.

-	~~{{STRUCTURE_1s6i\| PDB=1s6i \| SCENE= }}~~	+	Unexpected structure of the Ca2+-regulatory region from soybean calcium-dependent protein kinase-alpha.,Weljie AM, Vogel HJ J Biol Chem. 2004 Aug 20;279(34):35494-502. Epub 2004 May 20. PMID:15155727<ref>PMID:15155727</ref>

-	~~===Ca2+-regulatory region (CLD) from soybean calcium-dependent protein kinase-alpha (CDPK) in the presence~~ of ~~Ca2+ and~~ the ~~junction domain (JD)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_15155727}}~~	+	==See Also==
-		+	*[[Calcium-dependent protein kinase\|Calcium-dependent protein kinase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1s6i~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S6I OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:015155727<~~/~~ref~~><~~ref group="xtra">PMID:015568805</ref><references group="xtra"~~/>	+
	[[Category: Glycine max]]		[[Category: Glycine max]]
	[[Category: Vogel, H J.]]		[[Category: Vogel, H J.]]

OCA at 09:32, 16 January 2013

OCA — Wed, 16 Jan 2013 09:32:06 GMT

←Older revision		Revision as of 09:32, 16 January 2013
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	[[Image:1s6i.png\|left\|200px]]		[[Image:1s6i.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_1s6i\| PDB=1s6i \| SCENE= }}		{{STRUCTURE_1s6i\| PDB=1s6i \| SCENE= }}

	===Ca2+-regulatory region (CLD) from soybean calcium-dependent protein kinase-alpha (CDPK) in the presence of Ca2+ and the junction domain (JD)===		===Ca2+-regulatory region (CLD) from soybean calcium-dependent protein kinase-alpha (CDPK) in the presence of Ca2+ and the junction domain (JD)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15155727}}, adds the Publication Abstract to the page
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	{{ABSTRACT_PUBMED_15155727}}		{{ABSTRACT_PUBMED_15155727}}

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	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15155727~~</ref><ref group="xtra">PMID:~~15568805~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015155727</ref><ref group="xtra">PMID:015568805</ref><references group="xtra"/>
	[[Category: Glycine max]]		[[Category: Glycine max]]
	[[Category: Vogel, H J.]]		[[Category: Vogel, H J.]]