1q8d - Revision history

OCA at 06:02, 17 April 2024

OCA — Wed, 17 Apr 2024 06:02:09 GMT

←Older revision		Revision as of 06:02, 17 April 2024
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	<StructureSection load='1q8d' size='340' side='right'caption='[[1q8d]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1q8d' size='340' side='right'caption='[[1q8d]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q8d]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q8D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1Q8D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q8d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q8D FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MPD:(4S)~~-~~2-METHYL-2~~,~~4-PENTANEDIOL'>MPD</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]] 1.8Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">GFRA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])~~</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=1q8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8d OCA], [https://pdbe.org/1q8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q8d RCSB], [https://www.ebi.ac.uk/pdbsum/1q8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q8d 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=1q8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8d OCA], [~~http~~://pdbe.org/1q8d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1q8d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1q8d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1q8d ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GFRA1_RAT GFRA1_RAT]] Receptor for GDNF. Mediates the GDNF-induced autophosphorylation and activation of the RET receptor.	+	[https://www.uniprot.org/uniprot/GFRA1_RAT GFRA1_RAT] Receptor for GDNF. Mediates the GDNF-induced autophosphorylation and activation of the RET receptor.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		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=1q8d 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=1q8d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Glial cell line-derived neurotrophic factor (GDNF) binds to the GDNF family co-receptor alpha1 (GFRalpha1) and activates RET receptor tyrosine kinase. GFRalpha1 has a putative domain structure of three homologous cysteine-rich domains, where domains 2 and 3 make up a central domain responsible for GDNF binding. We report here the 1.8 A crystal structure of GFRalpha1 domain 3 showing a new protein fold. It is an all-alpha five-helix bundle with five disulfide bridges. The structure was used to model the homologous domain 2, the other half of the GDNF-binding fragment, and to construct the first structural model of the GDNF-GFRalpha1 interaction. Using site-directed mutagenesis, we identified closely spaced residues, Phe213, Arg224, Arg225 and Ile229, comprising a putative GDNF-binding surface. Mutating each one of them had slightly different effects on GDNF binding and RET phosphorylation. In addition, the R217E mutant bound GDNF equally well in the presence and absence of RET. Arg217 may thus be involved in the allosteric properties of GFRalpha1 or in binding RET.
-
-	The structure of GFRalpha1 domain 3 reveals new insights into GDNF binding and RET activation.,Leppanen VM, Bespalov MM, Runeberg-Roos P, Puurand U, Merits A, Saarma M, Goldman A EMBO J. 2004 Apr 7;23(7):1452-62. Epub 2004 Mar 25. PMID:15044950<ref>PMID:15044950</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1q8d" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bespalov~~, M M~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: Goldman, A]]	+	[[Category: Bespalov MM]]
-	[[Category: Leppanen~~, V M~~]]	+	[[Category: Goldman A]]
-	[[Category: Merits, A]]	+	[[Category: Leppanen VM]]
-	[[Category: Puurand, U]]	+	[[Category: Merits A]]
-	[[Category: Runeberg-Roos, P]]	+	[[Category: Puurand U]]
-	[[Category: Saarma, M]]	+	[[Category: Runeberg-Roos P]]
-	~~[[Category: All-alpha]]~~	+	[[Category: Saarma M]]
-	~~[[Category: Cys-rich]]~~	+
-	~~[[Category: Hormone-growth factor receptor complex~~]]	+

OCA at 07:45, 9 December 2020

OCA — Wed, 09 Dec 2020 07:45:36 GMT

←Older revision		Revision as of 07:45, 9 December 2020
Line 1:		Line 1:

	==The crystal structure of GDNF family co-receptor alpha 1 domain 3==		==The crystal structure of GDNF family co-receptor alpha 1 domain 3==
-	<StructureSection load='1q8d' size='340' side='right' caption='[[1q8d]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1q8d' size='340' side='right'caption='[[1q8d]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q8d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q8D OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Q8D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q8d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q8D OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Q8D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFRA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFRA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=1q8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8d OCA], [http://pdbe.org/1q8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q8d RCSB], [http://www.ebi.ac.uk/pdbsum/1q8d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q8d 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=1q8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8d OCA], [http://pdbe.org/1q8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q8d RCSB], [http://www.ebi.ac.uk/pdbsum/1q8d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q8d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Bespalov, M M]]		[[Category: Bespalov, M M]]
	[[Category: Goldman, A]]		[[Category: Goldman, A]]

OCA at 08:29, 24 February 2018

OCA — Sat, 24 Feb 2018 08:29:12 GMT

←Older revision		Revision as of 08:29, 24 February 2018
Line 1:		Line 1:
		+
	==The crystal structure of GDNF family co-receptor alpha 1 domain 3==		==The crystal structure of GDNF family co-receptor alpha 1 domain 3==
	<StructureSection load='1q8d' size='340' side='right' caption='[[1q8d]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1q8d' size='340' side='right' caption='[[1q8d]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFRA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFRA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=1q8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8d OCA], [http://pdbe.org/1q8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q8d RCSB], [http://www.ebi.ac.uk/pdbsum/1q8d 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=1q8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8d OCA], [http://pdbe.org/1q8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q8d RCSB], [http://www.ebi.ac.uk/pdbsum/1q8d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q8d 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/q8/1q8d_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q8/1q8d_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 00:11, 9 February 2016

OCA — Tue, 09 Feb 2016 00:11:20 GMT

←Older revision		Revision as of 00:11, 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=1q8d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:42, 10 September 2015

OCA — Thu, 10 Sep 2015 16:42:47 GMT

←Older revision		Revision as of 16:42, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1q8d' size='340' side='right' caption='[[1q8d]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1q8d' size='340' side='right' caption='[[1q8d]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q8d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q8D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q8d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q8D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFRA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 ~~Rattus norvegicus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFRA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</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=1q8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q8d RCSB], [http://www.ebi.ac.uk/pdbsum/1q8d 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=1q8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8d OCA], [http://pdbe.org/1q8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q8d RCSB], [http://www.ebi.ac.uk/pdbsum/1q8d PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1q8d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rattus norvegicus~~]]	+	[[Category: Buffalo rat]]
	[[Category: Bespalov, M M]]		[[Category: Bespalov, M M]]
	[[Category: Goldman, A]]		[[Category: Goldman, A]]

OCA at 03:06, 25 December 2014

OCA — Thu, 25 Dec 2014 03:06:46 GMT

←Older revision		Revision as of 03:06, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1q8d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q8D FirstGlance]. <br>		<table><tr><td colspan='2'>[[1q8d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q8D FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFRA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFRA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</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=1q8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q8d RCSB], [http://www.ebi.ac.uk/pdbsum/1q8d 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=1q8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q8d RCSB], [http://www.ebi.ac.uk/pdbsum/1q8d PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GFRA1_RAT GFRA1_RAT]] Receptor for GDNF. Mediates the GDNF-induced autophosphorylation and activation of the RET receptor.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Bespalov, M M.]]	+	[[Category: Bespalov, M M]]
-	[[Category: Goldman, A.]]	+	[[Category: Goldman, A]]
-	[[Category: Leppanen, V M.]]	+	[[Category: Leppanen, V M]]
-	[[Category: Merits, A.]]	+	[[Category: Merits, A]]
-	[[Category: Puurand, U.]]	+	[[Category: Puurand, U]]
-	[[Category: Runeberg-Roos, P.]]	+	[[Category: Runeberg-Roos, P]]
-	[[Category: Saarma, M.]]	+	[[Category: Saarma, M]]
	[[Category: All-alpha]]		[[Category: All-alpha]]
	[[Category: Cys-rich]]		[[Category: Cys-rich]]
	[[Category: Hormone-growth factor receptor complex]]		[[Category: Hormone-growth factor receptor complex]]

OCA at 14:17, 29 September 2014

OCA — Mon, 29 Sep 2014 14:17:15 GMT

←Older revision		Revision as of 14:17, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1q8d.~~png~~\|~~left~~\|200px]]	+	==The crystal structure of GDNF family co-receptor alpha 1 domain 3==
		+	<StructureSection load='1q8d' size='340' side='right' caption='[[1q8d]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1q8d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q8D FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GFRA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])</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=1q8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q8d RCSB], [http://www.ebi.ac.uk/pdbsum/1q8d 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/q8/1q8d_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 ==
		+	Glial cell line-derived neurotrophic factor (GDNF) binds to the GDNF family co-receptor alpha1 (GFRalpha1) and activates RET receptor tyrosine kinase. GFRalpha1 has a putative domain structure of three homologous cysteine-rich domains, where domains 2 and 3 make up a central domain responsible for GDNF binding. We report here the 1.8 A crystal structure of GFRalpha1 domain 3 showing a new protein fold. It is an all-alpha five-helix bundle with five disulfide bridges. The structure was used to model the homologous domain 2, the other half of the GDNF-binding fragment, and to construct the first structural model of the GDNF-GFRalpha1 interaction. Using site-directed mutagenesis, we identified closely spaced residues, Phe213, Arg224, Arg225 and Ile229, comprising a putative GDNF-binding surface. Mutating each one of them had slightly different effects on GDNF binding and RET phosphorylation. In addition, the R217E mutant bound GDNF equally well in the presence and absence of RET. Arg217 may thus be involved in the allosteric properties of GFRalpha1 or in binding RET.

-	~~{{STRUCTURE_1q8d\| PDB=1q8d \| SCENE= }}~~	+	The structure of GFRalpha1 domain 3 reveals new insights into GDNF binding and RET activation.,Leppanen VM, Bespalov MM, Runeberg-Roos P, Puurand U, Merits A, Saarma M, Goldman A EMBO J. 2004 Apr 7;23(7):1452-62. Epub 2004 Mar 25. PMID:15044950<ref>PMID:15044950</ref>

-	~~===The crystal structure~~ of ~~GDNF family co-receptor alpha 1 domain 3===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15044950}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1q8d]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rattus_norvegicus Rattus norvegicus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1Q8D OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015044950<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Bespalov, M M.]]		[[Category: Bespalov, M M.]]

OCA: Protected "1q8d" [edit=sysop:move=sysop]

OCA — Wed, 02 Jan 2013 10:05:42 GMT

Protected "1q8d" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:05, 2 January 2013

OCA at 10:05, 2 January 2013

OCA — Wed, 02 Jan 2013 10:05:39 GMT

←Older revision		Revision as of 10:05, 2 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1q8d.png\|left\|200px]]		[[Image:1q8d.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1q8d", 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_1q8d\| PDB=1q8d \| SCENE= }}		{{STRUCTURE_1q8d\| PDB=1q8d \| SCENE= }}

	===The crystal structure of GDNF family co-receptor alpha 1 domain 3===		===The crystal structure of GDNF family co-receptor alpha 1 domain 3===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15044950}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15044950 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15044950}}		{{ABSTRACT_PUBMED_15044950}}

	==About this Structure==		==About this Structure==
-	~~1Q8D~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q8D OCA].	+	[[1q8d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q8D OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15044950~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015044950</ref><references group="xtra"/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
	[[Category: Bespalov, M M.]]		[[Category: Bespalov, M M.]]
Line 34:		Line 22:
	[[Category: All-alpha]]		[[Category: All-alpha]]
	[[Category: Cys-rich]]		[[Category: Cys-rich]]
-		+	[[Category: Hormone-growth factor receptor complex]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 04:46:28 2009''~~	+

OCA at 02:46, 17 February 2009

OCA — Tue, 17 Feb 2009 02:46:30 GMT

←Older revision		Revision as of 02:46, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1Q8D is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q8D OCA].	+	1Q8D is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q8D OCA].

	==Reference==		==Reference==
-	The structure of GFRalpha1 domain 3 reveals new insights into GDNF binding and RET activation., Leppanen VM, Bespalov MM, Runeberg-Roos P, Puurand U, Merits A, Saarma M, Goldman A, EMBO J. 2004 Apr 7;23(7):1452-62. Epub 2004 Mar 25. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15044950 15044950]~~	+	<ref group="xtra">PMID:15044950</ref><references group="xtra"/>
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Single protein]]
	[[Category: Bespalov, M M.]]		[[Category: Bespalov, M M.]]
	[[Category: Goldman, A.]]		[[Category: Goldman, A.]]
Line 36:		Line 35:
	[[Category: Cys-rich]]		[[Category: Cys-rich]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 08~~:08:~~27 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 04:46:28 2009''