6vij - Revision history

OCA at 14:37, 6 March 2024

OCA — Wed, 06 Mar 2024 14:37:54 GMT

←Older revision		Revision as of 14:37, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='6vij' size='340' side='right'caption='[[6vij]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='6vij' size='340' side='right'caption='[[6vij]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vij]] 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=6VIJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VIJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vij]] 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=6VIJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VIJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GDP:GUANOSINE~~-~~5-DIPHOSPHATE'>GDP</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.95Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Rabl3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id~~=~~10090 LK3 transgenic mice])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=6vij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vij OCA], [~~http~~://pdbe.org/6vij PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vij RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vij PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vij ProSAT]</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=6vij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vij OCA], [https://pdbe.org/6vij PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vij RCSB], [https://www.ebi.ac.uk/pdbsum/6vij PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vij ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/RABL3_MOUSE RABL3_MOUSE]
-	~~The small GTPase RABL3 is an oncogene of unknown physiological function. Homozygous knockout alleles of mouse Rabl3 were embryonic lethal, but a viable hypomorphic allele (xiamen~~ [xm]) causing in-frame deletion of four amino acids from the interswitch region resulted in profound defects in lymphopoiesis. Impaired lymphoid progenitor development led to deficiencies of B cells, T cells, and natural killer (NK) cells in Rabl3 (xm/xm) mice. T cells and NK cells exhibited impaired cytolytic activity, and mice infected with mouse cytomegalovirus (MCMV) displayed elevated titers in the spleen. Myeloid cells were normal in number and function. Biophysical and crystallographic studies demonstrated that RABL3 formed a homodimer in solution via interactions between the effector binding surfaces on each subunit; monomers adopted a typical small G protein fold. RABL3(xm) displayed a large compensatory alteration in switch I, which adopted a beta-strand configuration normally provided by the deleted interswitch residues, thereby permitting homodimer formation. Dysregulated effector binding due to conformational changes in the switch I-interswitch-switch II module likely underlies the xm phenotype. One such effector may be GPR89, putatively an ion channel or G protein-coupled receptor (GPCR). RABL3, but not RABL3(xm), strongly associated with and stabilized GPR89, and an N-ethyl-N-nitrosourea (ENU)-induced mutation (explorer) in Gpr89 phenocopied Rabl3 (xm).	+
-		+
-	Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function.,Zhong X, Su L, Yang Y, Nair-Gill E, Tang M, Anderton P, Li X, Wang J, Zhan X, Tomchick DR, Brautigam CA, Moresco EMY, Choi JH, Beutler B Proc Natl Acad Sci U S A. 2020 Mar 27. pii: ~~2000703117. doi:, 10.1073~~/~~pnas.2000703117. PMID:32220963<ref>PMID:32220963</ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6vij" style="background-color:#fffaf0;"><~~/~~div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Beutler, B]]	+	[[Category: Beutler B]]
-	[[Category: Su, L]]	+	[[Category: Su L]]
-	[[Category: Tomchick~~, D R]]~~	+	[[Category: Tomchick DR]]
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Small gtpase~~]]	+

OCA at 07:15, 29 April 2020

OCA — Wed, 29 Apr 2020 07:15:13 GMT

←Older revision		Revision as of 07:15, 29 April 2020
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	<StructureSection load='6vij' size='340' side='right'caption='[[6vij]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='6vij' size='340' side='right'caption='[[6vij]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vij]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VIJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VIJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vij]] 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=6VIJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VIJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rabl3 ([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://proteopedia.org/fgij/fg.htm?mol=6vij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vij OCA], [http://pdbe.org/6vij PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vij RCSB], [http://www.ebi.ac.uk/pdbsum/6vij PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vij 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=6vij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vij OCA], [http://pdbe.org/6vij PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vij RCSB], [http://www.ebi.ac.uk/pdbsum/6vij PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vij ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Beutler, B]]		[[Category: Beutler, B]]
	[[Category: Su, L]]		[[Category: Su, L]]

OCA at 06:58, 8 April 2020

OCA — Wed, 08 Apr 2020 06:58:08 GMT

←Older revision		Revision as of 06:58, 8 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6vij is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of mouse RABL3 in complex with GDP==
		+	<StructureSection load='6vij' size='340' side='right'caption='[[6vij]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6vij]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VIJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VIJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=6vij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vij OCA], [http://pdbe.org/6vij PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vij RCSB], [http://www.ebi.ac.uk/pdbsum/6vij PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vij ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The small GTPase RABL3 is an oncogene of unknown physiological function. Homozygous knockout alleles of mouse Rabl3 were embryonic lethal, but a viable hypomorphic allele (xiamen [xm]) causing in-frame deletion of four amino acids from the interswitch region resulted in profound defects in lymphopoiesis. Impaired lymphoid progenitor development led to deficiencies of B cells, T cells, and natural killer (NK) cells in Rabl3 (xm/xm) mice. T cells and NK cells exhibited impaired cytolytic activity, and mice infected with mouse cytomegalovirus (MCMV) displayed elevated titers in the spleen. Myeloid cells were normal in number and function. Biophysical and crystallographic studies demonstrated that RABL3 formed a homodimer in solution via interactions between the effector binding surfaces on each subunit; monomers adopted a typical small G protein fold. RABL3(xm) displayed a large compensatory alteration in switch I, which adopted a beta-strand configuration normally provided by the deleted interswitch residues, thereby permitting homodimer formation. Dysregulated effector binding due to conformational changes in the switch I-interswitch-switch II module likely underlies the xm phenotype. One such effector may be GPR89, putatively an ion channel or G protein-coupled receptor (GPCR). RABL3, but not RABL3(xm), strongly associated with and stabilized GPR89, and an N-ethyl-N-nitrosourea (ENU)-induced mutation (explorer) in Gpr89 phenocopied Rabl3 (xm).

-	~~Authors: Su~~, L., Tomchick, ~~D.R.~~, ~~Beutler~~, B.	+	Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function.,Zhong X, Su L, Yang Y, Nair-Gill E, Tang M, Anderton P, Li X, Wang J, Zhan X, Tomchick DR, Brautigam CA, Moresco EMY, Choi JH, Beutler B Proc Natl Acad Sci U S A. 2020 Mar 27. pii: 2000703117. doi:, 10.1073/pnas.2000703117. PMID:32220963<ref>PMID:32220963</ref>

-	~~Description: Crystal structure~~ of ~~mouse RABL3 in complex with GDP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Tomchick, D.R]]~~	+	<div class="pdbe-citations 6vij" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Su, L~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Beutler, B]]		[[Category: Beutler, B]]
		+	[[Category: Su, L]]
		+	[[Category: Tomchick, D R]]
		+	[[Category: Immune system]]
		+	[[Category: Small gtpase]]

OCA at 08:20, 27 March 2020

OCA — Fri, 27 Mar 2020 08:20:35 GMT

←Older revision		Revision as of 08:20, 27 March 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Su, L., Tomchick, D.R., Beutler, B.		Authors: Su, L., Tomchick, D.R., Beutler, B.

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

OCA — Wed, 22 Jan 2020 14:31:41 GMT

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

←Older revision

Revision as of 14:31, 22 January 2020

OCA: New page: '''Unreleased structure''' The entry 6vij is ON HOLD Authors: Su, L., Tomchick, D.R., Beutler, B. Description: Crystal structure of mouse RABL3 in complex with GDP [[Category: Unreleas...

OCA — Wed, 22 Jan 2020 14:31:39 GMT

New page: '''Unreleased structure''' The entry 6vij is ON HOLD Authors: Su, L., Tomchick, D.R., Beutler, B. Description: Crystal structure of mouse RABL3 in complex with GDP [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 6vij is ON HOLD

Authors: Su, L., Tomchick, D.R., Beutler, B.

Description: Crystal structure of mouse RABL3 in complex with GDP
[[Category: Unreleased Structures]]
[[Category: Tomchick, D.R]]
[[Category: Su, L]]
[[Category: Beutler, B]]