1tvg - Revision history

OCA at 08:42, 14 February 2024

2024-02-14T08:42:26Z

←Older revision		Revision as of 08:42, 14 February 2024
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	<StructureSection load='1tvg' size='340' side='right'caption='[[1tvg]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1tvg' size='340' side='right'caption='[[1tvg]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tvg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TVG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tvg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TVG 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>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene></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=1tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tvg OCA], [https://pdbe.org/1tvg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tvg RCSB], [https://www.ebi.ac.uk/pdbsum/1tvg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tvg ProSAT], [https://www.topsan.org/Proteins/NESGC/1tvg TOPSAN]</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=1tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tvg OCA], [https://pdbe.org/1tvg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tvg RCSB], [https://www.ebi.ac.uk/pdbsum/1tvg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tvg ProSAT], [https://www.topsan.org/Proteins/NESGC/1tvg TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/IFT25_HUMAN IFT25_HUMAN]] Component of the IFT complex B required for sonic hedgehog/SHH signaling. May mediate transport of SHH components: required for the export of SMO and PTCH1 receptors out of the cilium and the accumulation of GLI2 at the ciliary tip in response to activation of the SHH pathway, suggesting it is involved in the dynamic transport of SHH signaling molecules within the cilium. Not required for ciliary assembly (By similarity).	+	[https://www.uniprot.org/uniprot/IFT25_HUMAN IFT25_HUMAN] Component of the IFT complex B required for sonic hedgehog/SHH signaling. May mediate transport of SHH components: required for the export of SMO and PTCH1 receptors out of the cilium and the accumulation of GLI2 at the ciliary tip in response to activation of the SHH pathway, suggesting it is involved in the dynamic transport of SHH signaling molecules within the cilium. Not required for ciliary assembly (By similarity).
	== 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=1tvg 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=1tvg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The structure of human protein HSPC034 has been determined by both solution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. Refinement of the NMR structure ensemble, using a Rosetta protocol in the absence of NMR restraints, resulted in significant improvements not only in structure quality, but also in molecular replacement (MR) performance with the raw X-ray diffraction data using MOLREP and Phaser. This method has recently been shown to be generally applicable with improved MR performance demonstrated for eight NMR structures refined using Rosetta (Qian et al., Nature 2007;450:259-264). Additionally, NMR structures of HSPC034 calculated by standard methods that include NMR restraints have improvements in the RMSD to the crystal structure and MR performance in the order DYANA, CYANA, XPLOR-NIH, and CNS with explicit water refinement (CNSw). Further Rosetta refinement of the CNSw structures, perhaps due to more thorough conformational sampling and/or a superior force field, was capable of finding alternative low energy protein conformations that were equally consistent with the NMR data according to the Recall, Precision, and F-measure (RPF) scores. On further examination, the additional MR-performance shortfall for NMR refined structures as compared with the X-ray structure were attributed, in part, to crystal-packing effects, real structural differences, and inferior hydrogen bonding in the NMR structures. A good correlation between a decrease in the number of buried unsatisfied hydrogen-bond donors and improved MR performance demonstrates the importance of hydrogen-bond terms in the force field for improving NMR structures. The superior hydrogen-bond network in Rosetta-refined structures demonstrates that correct identification of hydrogen bonds should be a critical goal of NMR structure refinement. Inclusion of nonbivalent hydrogen bonds identified from Rosetta structures as additional restraints in the structure calculation results in NMR structures with improved MR performance.
-
-	Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.,Ramelot TA, Raman S, Kuzin AP, Xiao R, Ma LC, Acton TB, Hunt JF, Montelione GT, Baker D, Kennedy MA Proteins. 2009 Apr;75(1):147-67. PMID:18816799<ref>PMID:18816799</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1tvg" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Acton~~, T B~~]]	+	[[Category: Acton TB]]
-	[[Category: Hunt~~, J F~~]]	+	[[Category: Hunt JF]]
-	[[Category: Kuzin~~, A P~~]]	+	[[Category: Kuzin AP]]
-	[[Category: Lee, I]]	+	[[Category: Lee I]]
-	[[Category: Montelione~~, G T]]~~	+	[[Category: Montelione GT]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Tong L]]
-	[[Category: Tong, L]]	+	[[Category: Vorobiev SM]]
-	[[Category: Vorobiev~~, S M]]~~	+
-	~~[[Category: Cell cycle]]~~	+
-	~~[[Category: Nesg]]~~	+
-	~~[[Category: PSI, Protein structure initiative~~]]	+

OCA at 09:33, 29 September 2021

2021-09-29T09:33:18Z

←Older revision		Revision as of 09:33, 29 September 2021
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	<StructureSection load='1tvg' size='340' side='right'caption='[[1tvg]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1tvg' size='340' side='right'caption='[[1tvg]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tvg]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1TVG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tvg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TVG 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>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</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>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene></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=1tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tvg OCA], [~~http~~://pdbe.org/1tvg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1tvg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1tvg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1tvg ProSAT], [~~http~~://www.topsan.org/Proteins/NESGC/1tvg TOPSAN]</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=1tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tvg OCA], [https://pdbe.org/1tvg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tvg RCSB], [https://www.ebi.ac.uk/pdbsum/1tvg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tvg ProSAT], [https://www.topsan.org/Proteins/NESGC/1tvg TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/IFT25_HUMAN IFT25_HUMAN]] Component of the IFT complex B required for sonic hedgehog/SHH signaling. May mediate transport of SHH components: required for the export of SMO and PTCH1 receptors out of the cilium and the accumulation of GLI2 at the ciliary tip in response to activation of the SHH pathway, suggesting it is involved in the dynamic transport of SHH signaling molecules within the cilium. Not required for ciliary assembly (By similarity).	+	[[https://www.uniprot.org/uniprot/IFT25_HUMAN IFT25_HUMAN]] Component of the IFT complex B required for sonic hedgehog/SHH signaling. May mediate transport of SHH components: required for the export of SMO and PTCH1 receptors out of the cilium and the accumulation of GLI2 at the ciliary tip in response to activation of the SHH pathway, suggesting it is involved in the dynamic transport of SHH signaling molecules within the cilium. Not required for ciliary assembly (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 13:34, 25 December 2019

2019-12-25T13:34:35Z

←Older revision		Revision as of 13:34, 25 December 2019
Line 1:		Line 1:

	==X-ray structure of human PP25 gene product, HSPC034. Northeast Structural Genomics Target HR1958.==		==X-ray structure of human PP25 gene product, HSPC034. Northeast Structural Genomics Target HR1958.==
-	<StructureSection load='1tvg' size='340' side='right' caption='[[1tvg]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1tvg' size='340' side='right'caption='[[1tvg]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1tvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TVG FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TVG FirstGlance]. <br>
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Acton, T B]]		[[Category: Acton, T B]]
	[[Category: Hunt, J F]]		[[Category: Hunt, J F]]

OCA at 08:25, 21 March 2018

2018-03-21T08:25:58Z

←Older revision		Revision as of 08:25, 21 March 2018
Line 1:		Line 1:
		+
	==X-ray structure of human PP25 gene product, HSPC034. Northeast Structural Genomics Target HR1958.==		==X-ray structure of human PP25 gene product, HSPC034. Northeast Structural Genomics Target HR1958.==
	<StructureSection load='1tvg' size='340' side='right' caption='[[1tvg]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1tvg' size='340' side='right' caption='[[1tvg]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1tvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TVG FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TVG 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>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</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>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene></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=1tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tvg OCA], [http://pdbe.org/1tvg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tvg RCSB], [http://www.ebi.ac.uk/pdbsum/1tvg PDBsum], [http://www.topsan.org/Proteins/NESGC/1tvg TOPSAN]</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=1tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tvg OCA], [http://pdbe.org/1tvg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tvg RCSB], [http://www.ebi.ac.uk/pdbsum/1tvg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tvg ProSAT], [http://www.topsan.org/Proteins/NESGC/1tvg TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tv/1tvg_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tv/1tvg_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>

OCA at 00:57, 10 February 2016

2016-02-10T00:57:04Z

←Older revision		Revision as of 00:57, 10 February 2016
Line 16:		Line 16:
	<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=1tvg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:46, 11 September 2015

2015-09-11T03:46:10Z

←Older revision		Revision as of 03:46, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1tvg' size='340' side='right' caption='[[1tvg]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1tvg' size='340' side='right' caption='[[1tvg]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TVG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TVG 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>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</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>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene></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=1tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tvg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tvg RCSB], [http://www.ebi.ac.uk/pdbsum/1tvg PDBsum], [http://www.topsan.org/Proteins/NESGC/1tvg TOPSAN]</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=1tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tvg OCA], [http://pdbe.org/1tvg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tvg RCSB], [http://www.ebi.ac.uk/pdbsum/1tvg PDBsum], [http://www.topsan.org/Proteins/NESGC/1tvg TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~HSB11_HUMAN HSB11_HUMAN~~]] Component of the IFT complex B required for sonic hedgehog/SHH signaling. May mediate transport of SHH components: required for the export of SMO and PTCH1 receptors out of the cilium and the accumulation of GLI2 at the ciliary tip in response to activation of the SHH pathway, suggesting it is involved in the dynamic transport of SHH signaling molecules within the cilium. Not required for ciliary assembly (By similarity).	+	[[http://www.uniprot.org/uniprot/IFT25_HUMAN IFT25_HUMAN]] Component of the IFT complex B required for sonic hedgehog/SHH signaling. May mediate transport of SHH components: required for the export of SMO and PTCH1 receptors out of the cilium and the accumulation of GLI2 at the ciliary tip in response to activation of the SHH pathway, suggesting it is involved in the dynamic transport of SHH signaling molecules within the cilium. Not required for ciliary assembly (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 26:		Line 26:
	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 1tvg" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Acton, T B]]		[[Category: Acton, T B]]
	[[Category: Hunt, J F]]		[[Category: Hunt, J F]]

OCA at 10:40, 25 December 2014

2014-12-25T10:40:17Z

←Older revision		Revision as of 10:40, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1tvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TVG FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TVG FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</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>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene></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=1tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tvg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tvg RCSB], [http://www.ebi.ac.uk/pdbsum/1tvg PDBsum], [http://www.topsan.org/Proteins/NESGC/1tvg TOPSAN]</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=1tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tvg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tvg RCSB], [http://www.ebi.ac.uk/pdbsum/1tvg PDBsum], [http://www.topsan.org/Proteins/NESGC/1tvg TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HSB11_HUMAN HSB11_HUMAN]] Component of the IFT complex B required for sonic hedgehog/SHH signaling. May mediate transport of SHH components: required for the export of SMO and PTCH1 receptors out of the cilium and the accumulation of GLI2 at the ciliary tip in response to activation of the SHH pathway, suggesting it is involved in the dynamic transport of SHH signaling molecules within the cilium. Not required for ciliary assembly (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Acton, T B.]]	+	[[Category: Acton, T B]]
-	[[Category: Hunt, J F.]]	+	[[Category: Hunt, J F]]
-	[[Category: Kuzin, A P.]]	+	[[Category: Kuzin, A P]]
-	[[Category: Lee, I.]]	+	[[Category: Lee, I]]
-	[[Category: Montelione, G T.]]	+	[[Category: Montelione, G T]]
-	[[Category: ~~NESG, Northeast~~ Structural ~~Genomics Consortium.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Tong, L.]]	+	[[Category: Tong, L]]
-	[[Category: Vorobiev, S M.]]	+	[[Category: Vorobiev, S M]]
	[[Category: Cell cycle]]		[[Category: Cell cycle]]
	[[Category: Nesg]]		[[Category: Nesg]]
-	[[Category: ~~Northeast structural genomics consortium]]~~	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category:~~ Protein structure initiative]]	+
-	~~[[Category: Psi]]~~	+
-	~~[[Category: Structural genomic~~]]	+

OCA at 21:44, 29 September 2014

2014-09-29T21:44:48Z

←Older revision		Revision as of 21:44, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1tvg.~~png\|left~~\|200px]]	+	==X-ray structure of human PP25 gene product, HSPC034. Northeast Structural Genomics Target HR1958.==
		+	<StructureSection load='1tvg' size='340' side='right' caption='[[1tvg]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1tvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TVG FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene><br>
		+	<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=1tvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tvg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tvg RCSB], [http://www.ebi.ac.uk/pdbsum/1tvg PDBsum], [http://www.topsan.org/Proteins/NESGC/1tvg TOPSAN]</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/tv/1tvg_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 ==
		+	The structure of human protein HSPC034 has been determined by both solution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. Refinement of the NMR structure ensemble, using a Rosetta protocol in the absence of NMR restraints, resulted in significant improvements not only in structure quality, but also in molecular replacement (MR) performance with the raw X-ray diffraction data using MOLREP and Phaser. This method has recently been shown to be generally applicable with improved MR performance demonstrated for eight NMR structures refined using Rosetta (Qian et al., Nature 2007;450:259-264). Additionally, NMR structures of HSPC034 calculated by standard methods that include NMR restraints have improvements in the RMSD to the crystal structure and MR performance in the order DYANA, CYANA, XPLOR-NIH, and CNS with explicit water refinement (CNSw). Further Rosetta refinement of the CNSw structures, perhaps due to more thorough conformational sampling and/or a superior force field, was capable of finding alternative low energy protein conformations that were equally consistent with the NMR data according to the Recall, Precision, and F-measure (RPF) scores. On further examination, the additional MR-performance shortfall for NMR refined structures as compared with the X-ray structure were attributed, in part, to crystal-packing effects, real structural differences, and inferior hydrogen bonding in the NMR structures. A good correlation between a decrease in the number of buried unsatisfied hydrogen-bond donors and improved MR performance demonstrates the importance of hydrogen-bond terms in the force field for improving NMR structures. The superior hydrogen-bond network in Rosetta-refined structures demonstrates that correct identification of hydrogen bonds should be a critical goal of NMR structure refinement. Inclusion of nonbivalent hydrogen bonds identified from Rosetta structures as additional restraints in the structure calculation results in NMR structures with improved MR performance.

-	~~{{STRUCTURE_1tvg\| PDB=1tvg \| SCENE= }}~~	+	Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.,Ramelot TA, Raman S, Kuzin AP, Xiao R, Ma LC, Acton TB, Hunt JF, Montelione GT, Baker D, Kennedy MA Proteins. 2009 Apr;75(1):147-67. PMID:18816799<ref>PMID:18816799</ref>

-	~~===X-ray structure of human PP25 gene product~~, ~~HSPC034. Northeast Structural Genomics Target HR1958.===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18816799}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1tvg]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018816799<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Acton, T B.]]		[[Category: Acton, T B.]]

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

2013-01-05T13:12:05Z

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

←Older revision

Revision as of 13:12, 5 January 2013

OCA at 13:12, 5 January 2013

2013-01-05T13:12:02Z

←Older revision		Revision as of 13:12, 5 January 2013
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-	{{Seed}}
	[[Image:1tvg.png\|left\|200px]]		[[Image:1tvg.png\|left\|200px]]

-	<!--
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-	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_1tvg\| PDB=1tvg \| SCENE= }}		{{STRUCTURE_1tvg\| PDB=1tvg \| SCENE= }}

	===X-ray structure of human PP25 gene product, HSPC034. Northeast Structural Genomics Target HR1958.===		===X-ray structure of human PP25 gene product, HSPC034. Northeast Structural Genomics Target HR1958.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18816799}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18816799 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18816799}}		{{ABSTRACT_PUBMED_18816799}}

	==About this Structure==		==About this Structure==
-	~~1TVG~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA].	+	[[1tvg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVG OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18816799~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018816799</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Acton, T B.]]		[[Category: Acton, T B.]]
Line 39:		Line 27:
	[[Category: Psi]]		[[Category: Psi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 10 22:14:00 2009''