3hwj - Revision history

OCA at 07:32, 6 September 2023

OCA — Wed, 06 Sep 2023 07:32:59 GMT

←Older revision		Revision as of 07:32, 6 September 2023
Line 1:		Line 1:

	==Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)==		==Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)==
-	<StructureSection load='3hwj' size='340' side='right'caption='[[3hwj]]' scene=''>	+	<StructureSection load='3hwj' size='340' side='right'caption='[[3hwj]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HWJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hwj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HWJ FirstGlance]. <br>
-	</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=3hwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwj OCA], [https://pdbe.org/3hwj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hwj RCSB], [https://www.ebi.ac.uk/pdbsum/3hwj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hwj ProSAT]</span></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]] 2.25Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=3hwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwj OCA], [https://pdbe.org/3hwj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hwj RCSB], [https://www.ebi.ac.uk/pdbsum/3hwj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hwj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MYCB2_MOUSE MYCB2_MOUSE] Probable E3 ubiquitin-protein ligase which mediates ubiquitination and subsequent proteasomal degradation of target proteins. May have a role during synaptogenesis; candidate for respiratory distress and ventilatory disorders that arise from defective neuronal control of breathing. May function as a facilitator or regulator of transcriptional activation by MYC.<ref>PMID:14729956</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		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=3hwj 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=3hwj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	PHR [PAM (protein associated with Myc)-HIW (Highwire)-RPM-1 (regulator of presynaptic morphology 1)] proteins are conserved, large multi-domain E3 ubiquitin ligases with modular architecture. PHR proteins presynaptically control synaptic growth and axon guidance and postsynaptically regulate endocytosis of glutamate receptors. Dysfunction of neuronal ubiquitin-mediated proteasomal degradation is implicated in various neurodegenerative diseases. PHR proteins are characterized by the presence of two PHR domains near the N-terminus, which are essential for proper localization and function. Structures of both the first and second PHR domains of Mus musculus (mouse) Phr1 (MYC binding protein 2, Mycbp2) have been determined, revealing a novel beta sandwich fold composed of 11 antiparallel beta-strands. Conserved loops decorate the apical side of the first PHR domain (MmPHR1), yielding a distinct conserved surface feature. The surface of the second PHR domain (MmPHR2), in contrast, lacks significant conservation. Importantly, the structure of MmPHR1 provides insights into a loss-of-function mutation, Gly1092-->Glu, observed in the Caenorhabditis elegans ortholog RPM-1.
		+
		+	Structures of PHR domains from Mus musculus Phr1 (Mycbp2) explain the loss-of-function mutation (Gly1092-->Glu) of the C. elegans ortholog RPM-1.,Sampathkumar P, Ozyurt SA, Miller SA, Bain KT, Rutter ME, Gheyi T, Abrams B, Wang Y, Atwell S, Luz JG, Thompson DA, Wasserman SR, Emtage JS, Park EC, Rongo C, Jin Y, Klemke RL, Sauder JM, Burley SK J Mol Biol. 2010 Apr 9;397(4):883-92. Epub 2010 Feb 13. PMID:20156452<ref>PMID:20156452</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 3hwj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ubiquitin protein ligase 3D structures\|Ubiquitin protein ligase 3D structures]]		*[[Ubiquitin protein ligase 3D structures\|Ubiquitin protein ligase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Mus musculus]]
	[[Category: Atwell S]]		[[Category: Atwell S]]
	[[Category: Bain KT]]		[[Category: Bain KT]]

OCA at 11:59, 30 March 2022

OCA — Wed, 30 Mar 2022 11:59:12 GMT

←Older revision		Revision as of 11:59, 30 March 2022
Line 1:		Line 1:

	==Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)==		==Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)==
-	<StructureSection load='3hwj' size='340' side='right' caption='[[3hwj]]~~, [[Resolution\|resolution]] 2.25Å~~' scene=''>	+	<StructureSection load='3hwj' size='340' side='right'caption='[[3hwj]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[3hwj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3HWJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HWJ FirstGlance]. <br>
-	</td></tr>~~<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene></td></tr>~~	+	</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=3hwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwj OCA], [https://pdbe.org/3hwj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hwj RCSB], [https://www.ebi.ac.uk/pdbsum/3hwj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hwj ProSAT]</span></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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gbw\|3gbw]]</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mycbp2, Pam, Phr1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=3hwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwj OCA], [~~http~~://pdbe.org/3hwj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3hwj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3hwj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3hwj ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[http://www.uniprot.org/uniprot/MYCB2_MOUSE MYCB2_MOUSE]] Probable E3 ubiquitin-protein ligase which mediates ubiquitination and subsequent proteasomal degradation of target proteins. May have a role during synaptogenesis; candidate for respiratory distress and ventilatory disorders that arise from defective neuronal control of breathing. May function as a facilitator or regulator of transcriptional activation by MYC.<ref>PMID:14729956</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 22:		Line 16:
	</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=3hwj 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=3hwj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	PHR [PAM (protein associated with Myc)-HIW (Highwire)-RPM-1 (regulator of presynaptic morphology 1)] proteins are conserved, large multi-domain E3 ubiquitin ligases with modular architecture. PHR proteins presynaptically control synaptic growth and axon guidance and postsynaptically regulate endocytosis of glutamate receptors. Dysfunction of neuronal ubiquitin-mediated proteasomal degradation is implicated in various neurodegenerative diseases. PHR proteins are characterized by the presence of two PHR domains near the N-terminus, which are essential for proper localization and function. Structures of both the first and second PHR domains of Mus musculus (mouse) Phr1 (MYC binding protein 2, Mycbp2) have been determined, revealing a novel beta sandwich fold composed of 11 antiparallel beta-strands. Conserved loops decorate the apical side of the first PHR domain (MmPHR1), yielding a distinct conserved surface feature. The surface of the second PHR domain (MmPHR2), in contrast, lacks significant conservation. Importantly, the structure of MmPHR1 provides insights into a loss-of-function mutation, Gly1092-->Glu, observed in the Caenorhabditis elegans ortholog RPM-1.
-
-	Structures of PHR domains from Mus musculus Phr1 (Mycbp2) explain the loss-of-function mutation (Gly1092-->Glu) of the C. elegans ortholog RPM-1.,Sampathkumar P, Ozyurt SA, Miller SA, Bain KT, Rutter ME, Gheyi T, Abrams B, Wang Y, Atwell S, Luz JG, Thompson DA, Wasserman SR, Emtage JS, Park EC, Rongo C, Jin Y, Klemke RL, Sauder JM, Burley SK J Mol Biol. 2010 Apr 9;397(4):883-92. Epub 2010 Feb 13. PMID:20156452<ref>PMID:20156452</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3hwj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Ubiquitin protein ligase\|Ubiquitin protein ligase]]	+	*[[Ubiquitin protein ligase 3D structures\|Ubiquitin protein ligase 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Large Structures]]
-	[[Category: Atwell, S]]	+	[[Category: Atwell S]]
-	[[Category: Bain~~, K T~~]]	+	[[Category: Bain KT]]
-	[[Category: Burley~~, S K~~]]	+	[[Category: Burley SK]]
-	[[Category: Gheyi, T]]	+	[[Category: Gheyi T]]
-	[[Category: Klemke~~, R L~~]]	+	[[Category: Klemke RL]]
-	[[Category: Miller~~, S A]]~~	+	[[Category: Miller SA]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Ozyurt SA]]
-	[[Category: Ozyurt~~, S A~~]]	+	[[Category: Rutter ME]]
-	[[Category: Rutter~~, M E~~]]	+	[[Category: Sampathkumar P]]
-	[[Category: Sampathkumar, P]]	+	[[Category: Sauder JM]]
-	[[Category: Sauder~~, J M~~]]	+	[[Category: Wasserman SR]]
-	[[Category: Wasserman~~, S R]]~~	+
-	~~[[Category: Alternative splicing]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Myc-binding protein 2]]~~	+
-	~~[[Category: Mycbp2]]~~	+
-	~~[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Pam]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Phr domain]]~~	+
-	~~[[Category: Phr protein]]~~	+
-	~~[[Category: Phr1]]~~	+
-	~~[[Category: Probable e3 ubiquitin-protein ligase mycbp2]]~~	+
-	~~[[Category: Protein associated with myc]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Ubl conjugation pathway]]~~	+
-	~~[[Category: Zinc]]~~	+
-	~~[[Category: Zinc-finger~~]]	+

OCA at 07:49, 12 December 2018

OCA — Wed, 12 Dec 2018 07:49:46 GMT

←Older revision		Revision as of 07:49, 12 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)==		==Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)==
	<StructureSection load='3hwj' size='340' side='right' caption='[[3hwj]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='3hwj' size='340' side='right' caption='[[3hwj]], [[Resolution\|resolution]] 2.25Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gbw\|3gbw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gbw\|3gbw]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mycbp2, Pam, Phr1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mycbp2, Pam, Phr1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=3hwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwj OCA], [http://pdbe.org/3hwj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hwj RCSB], [http://www.ebi.ac.uk/pdbsum/3hwj 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=3hwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwj OCA], [http://pdbe.org/3hwj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hwj RCSB], [http://www.ebi.ac.uk/pdbsum/3hwj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hwj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hw/3hwj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hw/3hwj_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 50:		Line 51:
	[[Category: Sauder, J M]]		[[Category: Sauder, J M]]
	[[Category: Wasserman, S R]]		[[Category: Wasserman, S R]]
		+	[[Category: Alternative splicing]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
Line 67:		Line 69:
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
	[[Category: Ubl conjugation pathway]]		[[Category: Ubl conjugation pathway]]
		+	[[Category: Zinc]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

OCA at 14:37, 8 February 2016

OCA — Mon, 08 Feb 2016 14:37:38 GMT

←Older revision		Revision as of 14:37, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3hwj' size='340' side='right' caption='[[3hwj]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='3hwj' size='340' side='right' caption='[[3hwj]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hwj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mus_musculus Mus musculus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HWJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hwj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HWJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gbw\|3gbw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gbw\|3gbw]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mycbp2, Pam, Phr1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 ~~Mus musculus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mycbp2, Pam, Phr1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=3hwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hwj RCSB], [http://www.ebi.ac.uk/pdbsum/3hwj 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=3hwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwj OCA], [http://pdbe.org/3hwj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hwj RCSB], [http://www.ebi.ac.uk/pdbsum/3hwj PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<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=3hwj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3hwj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mus musculus~~]]	+	[[Category: Lk3 transgenic mice]]
	[[Category: Atwell, S]]		[[Category: Atwell, S]]
	[[Category: Bain, K T]]		[[Category: Bain, K T]]

OCA at 00:04, 25 December 2014

OCA — Thu, 25 Dec 2014 00:04:08 GMT

←Older revision		Revision as of 00:04, 25 December 2014
Line 9:		Line 9:
	<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=3hwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hwj RCSB], [http://www.ebi.ac.uk/pdbsum/3hwj 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=3hwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hwj RCSB], [http://www.ebi.ac.uk/pdbsum/3hwj PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MYCB2_MOUSE MYCB2_MOUSE]] Probable E3 ubiquitin-protein ligase which mediates ubiquitination and subsequent proteasomal degradation of target proteins. May have a role during synaptogenesis; candidate for respiratory distress and ventilatory disorders that arise from defective neuronal control of breathing. May function as a facilitator or regulator of transcriptional activation by MYC.<ref>PMID:14729956</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 13:21, 6 November 2014

OCA — Thu, 06 Nov 2014 13:21:56 GMT

←Older revision		Revision as of 13:21, 6 November 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3hwj\| PDB=3hwj \| SCENE= }}~~	+	==Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)==
-	===Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)===	+	<StructureSection load='3hwj' size='340' side='right' caption='[[3hwj]], [[Resolution\|resolution]] 2.25Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20156452}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3hwj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HWJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gbw\|3gbw]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mycbp2, Pam, Phr1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</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=3hwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hwj RCSB], [http://www.ebi.ac.uk/pdbsum/3hwj 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/hw/3hwj_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 ==
		+	PHR [PAM (protein associated with Myc)-HIW (Highwire)-RPM-1 (regulator of presynaptic morphology 1)] proteins are conserved, large multi-domain E3 ubiquitin ligases with modular architecture. PHR proteins presynaptically control synaptic growth and axon guidance and postsynaptically regulate endocytosis of glutamate receptors. Dysfunction of neuronal ubiquitin-mediated proteasomal degradation is implicated in various neurodegenerative diseases. PHR proteins are characterized by the presence of two PHR domains near the N-terminus, which are essential for proper localization and function. Structures of both the first and second PHR domains of Mus musculus (mouse) Phr1 (MYC binding protein 2, Mycbp2) have been determined, revealing a novel beta sandwich fold composed of 11 antiparallel beta-strands. Conserved loops decorate the apical side of the first PHR domain (MmPHR1), yielding a distinct conserved surface feature. The surface of the second PHR domain (MmPHR2), in contrast, lacks significant conservation. Importantly, the structure of MmPHR1 provides insights into a loss-of-function mutation, Gly1092-->Glu, observed in the Caenorhabditis elegans ortholog RPM-1.

-	~~==About this Structure==~~	+	Structures of PHR domains from Mus musculus Phr1 (Mycbp2) explain the loss-of-function mutation (Gly1092-->Glu) of the C. elegans ortholog RPM-1.,Sampathkumar P, Ozyurt SA, Miller SA, Bain KT, Rutter ME, Gheyi T, Abrams B, Wang Y, Atwell S, Luz JG, Thompson DA, Wasserman SR, Emtage JS, Park EC, Rongo C, Jin Y, Klemke RL, Sauder JM, Burley SK J Mol Biol. 2010 Apr 9;397(4):883-92. Epub 2010 Feb 13. PMID:20156452<ref>PMID:20156452</ref>
-	~~[[3hwj]] is a 2 chain structure with sequence~~ from ~~[http://en.wikipedia.org/wiki/Mus_musculus~~ Mus musculus]. ~~Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3HWJ OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:020156452~~</~~ref~~><~~references group="xtra"~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Ubiquitin protein ligase\|Ubiquitin protein ligase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Atwell, S.]]	+	[[Category: Atwell, S]]
-	[[Category: Bain, K T.]]	+	[[Category: Bain, K T]]
-	[[Category: Burley, S K.]]	+	[[Category: Burley, S K]]
-	[[Category: Gheyi, T.]]	+	[[Category: Gheyi, T]]
-	[[Category: Klemke, R L.]]	+	[[Category: Klemke, R L]]
-	[[Category: Miller, S A.]]	+	[[Category: Miller, S A]]
-	[[Category: ~~NYSGXRC, New York SGX Research Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Ozyurt, S A.]]	+	[[Category: Ozyurt, S A]]
-	[[Category: Rutter, M E.]]	+	[[Category: Rutter, M E]]
-	[[Category: Sampathkumar, P.]]	+	[[Category: Sampathkumar, P]]
-	[[Category: Sauder, J M.]]	+	[[Category: Sauder, J M]]
-	[[Category: Wasserman, S R.]]	+	[[Category: Wasserman, S R]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Myc-binding protein 2]]		[[Category: Myc-binding protein 2]]
	[[Category: Mycbp2]]		[[Category: Mycbp2]]
-	[[Category: New ~~york sgx research center~~ for ~~structural genomic]]~~	+	[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
-	~~[[Category: New york structural genomix research consortium~~]]	+
	[[Category: Nucleus]]		[[Category: Nucleus]]
-	[[Category: Nysgxrc]]
	[[Category: Pam]]		[[Category: Pam]]
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
Line 36:		Line 60:
	[[Category: Probable e3 ubiquitin-protein ligase mycbp2]]		[[Category: Probable e3 ubiquitin-protein ligase mycbp2]]
	[[Category: Protein associated with myc]]		[[Category: Protein associated with myc]]
-	[[Category: Protein structure initiative]]	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category: Psi-2]]~~	+
-	~~[[Category: Structural genomic~~]]	+
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
	[[Category: Ubl conjugation pathway]]		[[Category: Ubl conjugation pathway]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

OCA: Protected "3hwj" [edit=sysop:move=sysop]

OCA — Wed, 13 Mar 2013 11:01:17 GMT

Protected "3hwj" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:01, 13 March 2013

OCA at 11:01, 13 March 2013

OCA — Wed, 13 Mar 2013 11:01:14 GMT

←Older revision		Revision as of 11:01, 13 March 2013
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-	{{Seed}}
-	[[Image:3hwj.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3hwj", 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_3hwj\| PDB=3hwj \| SCENE= }}		{{STRUCTURE_3hwj\| PDB=3hwj \| SCENE= }}
-
	===Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)===		===Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20156452}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20156452 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20156452}}		{{ABSTRACT_PUBMED_20156452}}

	==About this Structure==		==About this Structure==
-	~~3HWJ~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWJ OCA].	+	[[3hwj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWJ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20156452~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020156452</ref><references group="xtra"/>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Atwell, S.]]		[[Category: Atwell, S.]]
Line 37:		Line 21:
	[[Category: Sauder, J M.]]		[[Category: Sauder, J M.]]
	[[Category: Wasserman, S R.]]		[[Category: Wasserman, S R.]]
-	[[Category: Alternative splicing]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
Line 59:		Line 42:
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
	[[Category: Ubl conjugation pathway]]		[[Category: Ubl conjugation pathway]]
-	[[Category: Zinc]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 7 10:03:04 2010''

OCA at 07:03, 7 April 2010

OCA — Wed, 07 Apr 2010 07:03:04 GMT

←Older revision		Revision as of 07:03, 7 April 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3hwj.~~jpg~~\|left\|200px]]	+	[[Image:3hwj.png\|left\|200px]]

	<!--		<!--
Line 12:		Line 12:
	===Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)===		===Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20156452}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20156452 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20156452}}

	==About this Structure==		==About this Structure==
-	3HWJ is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWJ OCA].	+	3HWJ is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWJ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20156452</ref><references group="xtra"/>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Atwell, S.]]		[[Category: Atwell, S.]]
-	[[Category: Bain, K.]]	+	[[Category: Bain, K T.]]
	[[Category: Burley, S K.]]		[[Category: Burley, S K.]]
	[[Category: Gheyi, T.]]		[[Category: Gheyi, T.]]
-	[[Category: Klemke, R.]]	+	[[Category: Klemke, R L.]]
-	[[Category: Miller, S.]]	+	[[Category: Miller, S A.]]
	[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics.]]		[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics.]]
-	[[Category: Ozyurt, S.]]	+	[[Category: Ozyurt, S A.]]
-	[[Category: Rutter, M.]]	+	[[Category: Rutter, M E.]]
	[[Category: Sampathkumar, P.]]		[[Category: Sampathkumar, P.]]
	[[Category: Sauder, J M.]]		[[Category: Sauder, J M.]]
-	[[Category: Wasserman, S.]]	+	[[Category: Wasserman, S R.]]
	[[Category: Alternative splicing]]		[[Category: Alternative splicing]]
	[[Category: Ligase]]		[[Category: Ligase]]
Line 53:		Line 62:
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 22 20~~:44:~~45 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 7 10:03:04 2010''

OCA at 17:44, 22 July 2009

OCA — Wed, 22 Jul 2009 17:44:47 GMT

←Older revision		Revision as of 17:44, 22 July 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3hwj.jpg\|left\|200px]]

-	The ~~entry 3hwj~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3hwj", 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_3hwj\| PDB=3hwj \| SCENE= }}

-	Authors: Sampathkumar, P., Ozyurt, S., Wasserman, S., Miller, S., Bain, K., Rutter, M., Tarun, G., Klemke, R., Atwell, S., Sauder, J.M., Burley, S.K., New York SGX Research Center for Structural Genomics (~~NYSGXRC~~)	+	===Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)===

-	Description: Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul ~~1 08~~:57:07 2009''	+	==About this Structure==
		+	3HWJ is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWJ OCA].
		+	[[Category: Mus musculus]]
		+	[[Category: Atwell, S.]]
		+	[[Category: Bain, K.]]
		+	[[Category: Burley, S K.]]
		+	[[Category: Gheyi, T.]]
		+	[[Category: Klemke, R.]]
		+	[[Category: Miller, S.]]
		+	[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics.]]
		+	[[Category: Ozyurt, S.]]
		+	[[Category: Rutter, M.]]
		+	[[Category: Sampathkumar, P.]]
		+	[[Category: Sauder, J M.]]
		+	[[Category: Wasserman, S.]]
		+	[[Category: Alternative splicing]]
		+	[[Category: Ligase]]
		+	[[Category: Metal-binding]]
		+	[[Category: Myc-binding protein 2]]
		+	[[Category: Mycbp2]]
		+	[[Category: New york sgx research center for structural genomic]]
		+	[[Category: New york structural genomix research consortium]]
		+	[[Category: Nucleus]]
		+	[[Category: Nysgxrc]]
		+	[[Category: Pam]]
		+	[[Category: Phosphoprotein]]
		+	[[Category: Phr domain]]
		+	[[Category: Phr protein]]
		+	[[Category: Phr1]]
		+	[[Category: Probable e3 ubiquitin-protein ligase mycbp2]]
		+	[[Category: Protein associated with myc]]
		+	[[Category: Protein structure initiative]]
		+	[[Category: Psi-2]]
		+	[[Category: Structural genomic]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription regulation]]
		+	[[Category: Ubl conjugation pathway]]
		+	[[Category: Zinc]]
		+	[[Category: Zinc-finger]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 22 20:44:45 2009''