6x1n - Revision history

OCA at 14:40, 18 October 2023

OCA — Wed, 18 Oct 2023 14:40:41 GMT

←Older revision		Revision as of 14:40, 18 October 2023
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	==Crystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1 PDZ3 (mbDLG-3)==		==Crystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1 PDZ3 (mbDLG-3)==
-	<StructureSection load='6x1n' size='340' side='right'caption='[[6x1n]]' scene=''>	+	<StructureSection load='6x1n' size='340' side='right'caption='[[6x1n]], [[Resolution\|resolution]] 1.40Å' 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=6X1N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6X1N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6x1n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Monosiga_brevicollis Monosiga brevicollis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6X1N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6X1N FirstGlance]. <br>
-	</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=6x1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6x1n OCA], [~~http~~://pdbe.org/6x1n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6x1n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6x1n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6x1n 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]] 1.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6x1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6x1n OCA], [https://pdbe.org/6x1n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6x1n RCSB], [https://www.ebi.ac.uk/pdbsum/6x1n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6x1n ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A9UT73_MONBE A9UT73_MONBE]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Identification of the molecular networks that facilitated the evolution of multicellular animals from their unicellular ancestors is a fundamental problem in evolutionary cellular biology. Choanoflagellates are recognized as the closest extant nonmetazoan ancestors to animals. These unicellular eukaryotes can adopt a multicellular-like "rosette" state. Therefore, they are compelling models for the study of early multicellularity. Comparative studies revealed that a number of putative human orthologs are present in choanoflagellate genomes, suggesting that a subset of these genes were necessary for the emergence of multicellularity. However, previous work is largely based on sequence alignments alone, which does not confirm structural nor functional similarity. Here, we focus on the PDZ domain, a peptide-binding domain which plays critical roles in myriad cellular signaling networks and which underwent a gene family expansion in metazoan lineages. Using a customized sequence similarity search algorithm, we identified 178 PDZ domains in the Monosiga brevicollis proteome. This includes 11 previously unidentified sequences, which we analyzed using Rosetta and homology modeling. To assess conservation of protein structure, we solved high-resolution crystal structures of representative M. brevicollis PDZ domains that are homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains. To assess functional conservation, we calculated binding affinities for mbGIPC, mbSHANK1, mbSNX27, and mbDLG-3 PDZ domains from M. brevicollis. Overall, we find that peptide selectivity is generally conserved between these two disparate organisms, with one possible exception, mbDLG-3. Overall, our results provide novel insight into signaling pathways in a choanoflagellate model of primitive multicellularity.
		+
		+	Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis.,Gao M, Mackley IGP, Mesbahi-Vasey S, Bamonte HA, Struyvenberg SA, Landolt L, Pederson NJ, Williams LI, Bahl CD, Brooks L 3rd, Amacher JF Protein Sci. 2020 Nov;29(11):2226-2244. doi: 10.1002/pro.3947. Epub 2020 Sep 25. PMID:32914530<ref>PMID:32914530</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6x1n" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Monosiga brevicollis]]
	[[Category: Amacher JF]]		[[Category: Amacher JF]]
	[[Category: Mackley I]]		[[Category: Mackley I]]

OCA at 06:55, 25 November 2020

OCA — Wed, 25 Nov 2020 06:55:09 GMT

←Older revision		Revision as of 06:55, 25 November 2020
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-	'''Unreleased structure'''

-	~~The entry 6x1n is ON HOLD until Paper Publication~~	+	==Crystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1 PDZ3 (mbDLG-3)==
-		+	<StructureSection load='6x1n' size='340' side='right'caption='[[6x1n]]' scene=''>
-	~~Authors: Mackley, I., Amacher, J.F.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6X1N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6X1N FirstGlance]. <br>
-	~~Description:~~ Crystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1 PDZ3 (mbDLG-3)	+	</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=6x1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6x1n OCA], [http://pdbe.org/6x1n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6x1n RCSB], [http://www.ebi.ac.uk/pdbsum/6x1n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6x1n ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Amacher~~, J.F~~]]	+	__TOC__
-	[[Category: Mackley, I]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Amacher JF]]
		+	[[Category: Mackley I]]

OCA at 18:19, 24 June 2020

OCA — Wed, 24 Jun 2020 18:19:22 GMT

←Older revision		Revision as of 18:19, 24 June 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6x1n is ON HOLD	+	The entry 6x1n is ON HOLD until Paper Publication

	Authors: Mackley, I., Amacher, J.F.		Authors: Mackley, I., Amacher, J.F.

OCA: Protected "6x1n" [edit=sysop:move=sysop]

OCA — Wed, 27 May 2020 04:52:44 GMT

Protected "6x1n" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:52, 27 May 2020

OCA: New page: '''Unreleased structure''' The entry 6x1n is ON HOLD Authors: Mackley, I., Amacher, J.F. Description: Crystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1 PDZ3 (mbDLG-3) [...

OCA — Wed, 27 May 2020 04:52:41 GMT

New page: '''Unreleased structure''' The entry 6x1n is ON HOLD Authors: Mackley, I., Amacher, J.F. Description: Crystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1 PDZ3 (mbDLG-3) [...

New page

'''Unreleased structure'''

The entry 6x1n is ON HOLD

Authors: Mackley, I., Amacher, J.F.

Description: Crystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1 PDZ3 (mbDLG-3)
[[Category: Unreleased Structures]]
[[Category: Amacher, J.F]]
[[Category: Mackley, I]]