1ts8 - Revision history

OCA at 08:44, 1 May 2024

OCA — Wed, 01 May 2024 08:44:13 GMT

←Older revision		Revision as of 08:44, 1 May 2024
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	<StructureSection load='1ts8' size='340' side='right'caption='[[1ts8]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1ts8' size='340' side='right'caption='[[1ts8]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ts8]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Dsm_244 Dsm 244~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TS8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1TS8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ts8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TS8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TS8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=HC4:4~~-~~HYDROXYCINNAMIC+ACID'>HC4</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]] 1.6Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]]~~</~~div~~>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])~~</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=1ts8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ts8 OCA], [https://pdbe.org/1ts8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ts8 RCSB], [https://www.ebi.ac.uk/pdbsum/1ts8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ts8 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=1ts8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ts8 OCA], [~~http~~://pdbe.org/1ts8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ts8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ts8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ts8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA]] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.	+	[https://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
	== 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=1ts8 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=1ts8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Determining 3D intermediate structures during the biological action of proteins in real time under ambient conditions is essential for understanding how proteins function. Here we use time-resolved Laue crystallography to extract short-lived intermediate structures and thereby unveil signal transduction in the blue light photoreceptor photoactive yellow protein (PYP) from Halorhodospira halophila. By analyzing a comprehensive set of Laue data during the PYP photocycle (forty-seven time points from one nanosecond to one second), we track all atoms in PYP during its photocycle and directly observe how absorption of a blue light photon by its p-coumaric acid chromophore triggers a reversible photocycle. We identify a complex chemical mechanism characterized by five distinct structural intermediates. Structural changes at the chromophore in the early, red-shifted intermediates are transduced to the exterior of the protein in the late, blue-shifted intermediates through an initial "volume-conserving" isomerization of the chromophore and the progressive disruption of hydrogen bonds between the chromophore and its surrounding binding pocket. These results yield a comprehensive view of the PYP photocycle when seen in the light of previous biophysical studies on the system.
-
-	Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds.,Ihee H, Rajagopal S, Srajer V, Pahl R, Anderson S, Schmidt M, Schotte F, Anfinrud PA, Wulff M, Moffat K Proc Natl Acad Sci U S A. 2005 May 17;102(20):7145-50. Epub 2005 May 3. PMID:15870207<ref>PMID:15870207</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ts8" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dsm 244~~]]	+	[[Category: Halorhodospira halophila]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Anderson, S]]	+	[[Category: Anderson S]]
-	[[Category: Anfinrud~~, P A~~]]	+	[[Category: Anfinrud PA]]
-	[[Category: Ihee, H]]	+	[[Category: Ihee H]]
-	[[Category: Moffat, K]]	+	[[Category: Moffat K]]
-	[[Category: Pahl, R]]	+	[[Category: Pahl R]]
-	[[Category: Rajagopal, S]]	+	[[Category: Rajagopal S]]
-	[[Category: Schmidt, M]]	+	[[Category: Schmidt M]]
-	[[Category: Schotte, F]]	+	[[Category: Schotte F]]
-	[[Category: Srajer, V]]	+	[[Category: Srajer V]]
-	[[Category: Wulff, M]]	+	[[Category: Wulff M]]
-	~~[[Category: Photoreceptor~~]]	+

OCA at 11:59, 24 December 2020

OCA — Thu, 24 Dec 2020 11:59:03 GMT

←Older revision		Revision as of 11:59, 24 December 2020
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	==Structure of the pR cis planar intermediate from time-resolved Laue crystallography==		==Structure of the pR cis planar intermediate from time-resolved Laue crystallography==
-	<StructureSection load='1ts8' size='340' side='right' caption='[[1ts8]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1ts8' size='340' side='right'caption='[[1ts8]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ts8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_244 Dsm 244]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TS8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1TS8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ts8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_244 Dsm 244]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TS8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1TS8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])</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=1ts8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ts8 OCA], [http://pdbe.org/1ts8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ts8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ts8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ts8 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=1ts8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ts8 OCA], [http://pdbe.org/1ts8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ts8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ts8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ts8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ts/1ts8_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ts/1ts8_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 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Dsm 244]]		[[Category: Dsm 244]]
		+	[[Category: Large Structures]]
	[[Category: Anderson, S]]		[[Category: Anderson, S]]
	[[Category: Anfinrud, P A]]		[[Category: Anfinrud, P A]]

OCA at 09:49, 12 October 2017

OCA — Thu, 12 Oct 2017 09:49:23 GMT

←Older revision		Revision as of 09:49, 12 October 2017
Line 1:		Line 1:
		+
	==Structure of the pR cis planar intermediate from time-resolved Laue crystallography==		==Structure of the pR cis planar intermediate from time-resolved Laue crystallography==
	<StructureSection load='1ts8' size='340' side='right' caption='[[1ts8]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1ts8' size='340' side='right' caption='[[1ts8]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])</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=1ts8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ts8 OCA], [http://pdbe.org/1ts8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ts8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ts8 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=1ts8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ts8 OCA], [http://pdbe.org/1ts8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ts8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ts8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ts8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 21:14, 9 February 2016

OCA — Tue, 09 Feb 2016 21:14:57 GMT

←Older revision		Revision as of 21:14, 9 February 2016
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])</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=1ts8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ts8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ts8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ts8 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=1ts8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ts8 OCA], [http://pdbe.org/1ts8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ts8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ts8 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=1ts8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	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 1ts8" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:57, 9 September 2015

OCA — Wed, 09 Sep 2015 04:57:28 GMT

←Older revision		Revision as of 04:57, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1ts8' size='340' side='right' caption='[[1ts8]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1ts8' size='340' side='right' caption='[[1ts8]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ts8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Halorhodospira_halophila Halorhodospira halophila~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TS8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ts8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_244 Dsm 244]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TS8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 ~~Halorhodospira halophila~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])</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=1ts8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ts8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ts8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ts8 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=1ts8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ts8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ts8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ts8 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA]] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Halorhodospira halophila~~]]	+	[[Category: Dsm 244]]
	[[Category: Anderson, S]]		[[Category: Anderson, S]]
	[[Category: Anfinrud, P A]]		[[Category: Anfinrud, P A]]

OCA at 13:07, 6 January 2015

OCA — Tue, 06 Jan 2015 13:07:55 GMT

←Older revision		Revision as of 13:07, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ts8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TS8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ts8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TS8 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 Halorhodospira halophila])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 Halorhodospira halophila])</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=1ts8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ts8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ts8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ts8 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=1ts8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ts8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ts8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ts8 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Halorhodospira halophila]]		[[Category: Halorhodospira halophila]]
-	[[Category: Anderson, S.]]	+	[[Category: Anderson, S]]
-	[[Category: Anfinrud, P A.]]	+	[[Category: Anfinrud, P A]]
-	[[Category: Ihee, H.]]	+	[[Category: Ihee, H]]
-	[[Category: Moffat, K.]]	+	[[Category: Moffat, K]]
-	[[Category: Pahl, R.]]	+	[[Category: Pahl, R]]
-	[[Category: Rajagopal, S.]]	+	[[Category: Rajagopal, S]]
-	[[Category: Schmidt, M.]]	+	[[Category: Schmidt, M]]
-	[[Category: Schotte, F.]]	+	[[Category: Schotte, F]]
-	[[Category: Srajer, V.]]	+	[[Category: Srajer, V]]
-	[[Category: Wulff, M.]]	+	[[Category: Wulff, M]]
	[[Category: Photoreceptor]]		[[Category: Photoreceptor]]

OCA at 20:41, 29 September 2014

OCA — Mon, 29 Sep 2014 20:41:24 GMT

←Older revision		Revision as of 20:41, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1ts8.~~png~~\|~~left~~\|200px]]	+	==Structure of the pR cis planar intermediate from time-resolved Laue crystallography==
		+	<StructureSection load='1ts8' size='340' side='right' caption='[[1ts8]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ts8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TS8 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ts0\|1ts0]], [[1ts6\|1ts6]], [[1ts7\|1ts7]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 Halorhodospira halophila])</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=1ts8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ts8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ts8 RCSB], [http://www.ebi.ac.uk/pdbsum/1ts8 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/ts/1ts8_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 ==
		+	Determining 3D intermediate structures during the biological action of proteins in real time under ambient conditions is essential for understanding how proteins function. Here we use time-resolved Laue crystallography to extract short-lived intermediate structures and thereby unveil signal transduction in the blue light photoreceptor photoactive yellow protein (PYP) from Halorhodospira halophila. By analyzing a comprehensive set of Laue data during the PYP photocycle (forty-seven time points from one nanosecond to one second), we track all atoms in PYP during its photocycle and directly observe how absorption of a blue light photon by its p-coumaric acid chromophore triggers a reversible photocycle. We identify a complex chemical mechanism characterized by five distinct structural intermediates. Structural changes at the chromophore in the early, red-shifted intermediates are transduced to the exterior of the protein in the late, blue-shifted intermediates through an initial "volume-conserving" isomerization of the chromophore and the progressive disruption of hydrogen bonds between the chromophore and its surrounding binding pocket. These results yield a comprehensive view of the PYP photocycle when seen in the light of previous biophysical studies on the system.

-	~~{{STRUCTURE_1ts8\| PDB=1ts8 \| SCENE= }}~~	+	Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds.,Ihee H, Rajagopal S, Srajer V, Pahl R, Anderson S, Schmidt M, Schotte F, Anfinrud PA, Wulff M, Moffat K Proc Natl Acad Sci U S A. 2005 May 17;102(20):7145-50. Epub 2005 May 3. PMID:15870207<ref>PMID:15870207</ref>

-	~~===Structure~~ of the ~~pR cis planar intermediate from time-resolved Laue crystallography===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15870207}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1ts8]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Halorhodospira_halophila Halorhodospira halophila]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1TS8 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015870207<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Halorhodospira halophila]]		[[Category: Halorhodospira halophila]]
	[[Category: Anderson, S.]]		[[Category: Anderson, S.]]

OCA: Protected "1ts8" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 11:29:53 GMT

Protected "1ts8" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:29, 5 January 2013

OCA at 11:29, 5 January 2013

OCA — Sat, 05 Jan 2013 11:29:49 GMT

←Older revision		Revision as of 11:29, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1ts8.png\|left\|200px]]		[[Image:1ts8.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1ts8", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1ts8\| PDB=1ts8 \| SCENE= }}		{{STRUCTURE_1ts8\| PDB=1ts8 \| SCENE= }}

	===Structure of the pR cis planar intermediate from time-resolved Laue crystallography===		===Structure of the pR cis planar intermediate from time-resolved Laue crystallography===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15870207}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15870207 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15870207}}		{{ABSTRACT_PUBMED_15870207}}

	==About this Structure==		==About this Structure==
-	~~1TS8~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TS8 OCA].	+	[[1ts8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TS8 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15870207~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015870207</ref><references group="xtra"/>
	[[Category: Halorhodospira halophila]]		[[Category: Halorhodospira halophila]]
	[[Category: Anderson, S.]]		[[Category: Anderson, S.]]
Line 36:		Line 24:
	[[Category: Wulff, M.]]		[[Category: Wulff, M.]]
	[[Category: Photoreceptor]]		[[Category: Photoreceptor]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:48:13 2009''

OCA at 10:48, 17 February 2009

OCA — Tue, 17 Feb 2009 10:48:14 GMT

←Older revision		Revision as of 10:48, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1TS8 is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TS8 OCA].	+	1TS8 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TS8 OCA].

	==Reference==		==Reference==
-	Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds., Ihee H, Rajagopal S, Srajer V, Pahl R, Anderson S, Schmidt M, Schotte F, Anfinrud PA, Wulff M, Moffat K, Proc Natl Acad Sci U S A. 2005 May 17;102(20):7145-50. Epub 2005 May 3. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15870207 15870207]~~	+	<ref group="xtra">PMID:15870207</ref><references group="xtra"/>
	[[Category: Halorhodospira halophila]]		[[Category: Halorhodospira halophila]]
-	[[Category: Single protein]]
	[[Category: Anderson, S.]]		[[Category: Anderson, S.]]
	[[Category: Anfinrud, P A.]]		[[Category: Anfinrud, P A.]]
Line 38:		Line 37:
	[[Category: Photoreceptor]]		[[Category: Photoreceptor]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 10~~ 12:39:~~00 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:48:13 2009''