4xsq - Revision history

OCA at 17:50, 26 April 2023

OCA — Wed, 26 Apr 2023 17:50:30 GMT

←Older revision		Revision as of 17:50, 26 April 2023
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	<StructureSection load='4xsq' size='340' side='right'caption='[[4xsq]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='4xsq' size='340' side='right'caption='[[4xsq]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xsq]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Amphioxus Amphioxus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XSQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XSQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xsq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Branchiostoma_floridae Branchiostoma floridae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XSQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XSQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4xsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xsq OCA], [https://pdbe.org/4xsq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xsq RCSB], [https://www.ebi.ac.uk/pdbsum/4xsq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xsq ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRAFLDRAFT_66946 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7739 Amphioxus])~~</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=4xsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xsq OCA], [~~http~~://pdbe.org/4xsq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xsq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xsq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xsq ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/LRRCB_BRAFL LRRCB_BRAFL] Binds selectively to the Gram-positive bacteria S.aureus and S.pneumoniae. Does not adhere to the Gram-negative bacteria E.coli and S.enterica. Probably recognizes peptidoglycans expressed on the bacterial cell surface.<ref>PMID:26821753</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Amphioxus~~]]	+	[[Category: Branchiostoma floridae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cao~~, D D~~]]	+	[[Category: Cao DD]]
-	[[Category: Chen, Y]]	+	[[Category: Chen Y]]
-	[[Category: Cheng, W]]	+	[[Category: Cheng W]]
-	[[Category: Jiang~~, Y L~~]]	+	[[Category: Jiang YL]]
-	[[Category: Li, Q]]	+	[[Category: Li Q]]
-	[[Category: Wang~~, W J~~]]	+	[[Category: Wang WJ]]
-	[[Category: Zhou~~, C Z]]~~	+	[[Category: Zhou CZ]]
-	~~[[Category: Bf66946]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Leucine rich repeat]]~~	+
-	~~[[Category: Variable lymphocyte receptor~~]]	+

OCA at 00:13, 6 June 2019

OCA — Thu, 06 Jun 2019 00:13:05 GMT

←Older revision		Revision as of 00:13, 6 June 2019
Line 1:		Line 1:

	==Structure of a variable lymphocyte receptor-like protein Bf66946 from Branchiostoma floridae==		==Structure of a variable lymphocyte receptor-like protein Bf66946 from Branchiostoma floridae==
-	<StructureSection load='4xsq' size='340' side='right' caption='[[4xsq]], [[Resolution\|resolution]] 1.79Å' scene=''>	+	<StructureSection load='4xsq' size='340' side='right'caption='[[4xsq]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xsq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XSQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XSQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xsq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Amphioxus Amphioxus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XSQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XSQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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='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=4xsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xsq OCA], [http://pdbe.org/4xsq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xsq RCSB], [http://www.ebi.ac.uk/pdbsum/4xsq PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRAFLDRAFT_66946 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7739 Amphioxus])</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=4xsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xsq OCA], [http://pdbe.org/4xsq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xsq RCSB], [http://www.ebi.ac.uk/pdbsum/4xsq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xsq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Amphioxus]]
		+	[[Category: Large Structures]]
	[[Category: Cao, D D]]		[[Category: Cao, D D]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]
Line 28:		Line 31:
	[[Category: Wang, W J]]		[[Category: Wang, W J]]
	[[Category: Zhou, C Z]]		[[Category: Zhou, C Z]]
-	[[Category: Amphioxus]]
	[[Category: Bf66946]]		[[Category: Bf66946]]
	[[Category: Immune system]]		[[Category: Immune system]]
	[[Category: Leucine rich repeat]]		[[Category: Leucine rich repeat]]
	[[Category: Variable lymphocyte receptor]]		[[Category: Variable lymphocyte receptor]]

OCA at 12:56, 11 May 2016

OCA — Wed, 11 May 2016 12:56:07 GMT

←Older revision		Revision as of 12:56, 11 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4xsq is ~~ON HOLD~~	+	==Structure of a variable lymphocyte receptor-like protein Bf66946 from Branchiostoma floridae==
		+	<StructureSection load='4xsq' size='340' side='right' caption='[[4xsq]], [[Resolution\|resolution]] 1.79Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xsq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XSQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XSQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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='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=4xsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xsq OCA], [http://pdbe.org/4xsq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xsq RCSB], [http://www.ebi.ac.uk/pdbsum/4xsq PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Discovery of variable lymphocyte receptors (VLRs) in agnathans (jawless fish) has brought the origin of adaptive immunity system (AIS) forward to 500 million years ago accompanying with the emergence of vertebrates. Previous findings indicated that amphioxus, a representative model organism of chordate, also possesses some homologs of the basic components of TCR/BCR-based AIS, but it remains unknown if there exist any components of VLR-based AIS in amphioxus. Bioinformatics analyses revealed the amphioxus Branchiostoma floridae encodes a group of putative VLR-like proteins. Here we reported the 1.79 A crystal structure of Bf66946, which forms a crescent-shaped structure of five leucine-rich repeats (LRRs). Structural comparisons indicated that Bf66946 resembles the lamprey VLRC. Further electrostatic potential analyses showed a negatively-charged patch at the concave of LRR solenoid structure that might be responsible for antigen recognition. Site-directed mutagenesis combined with bacterial binding assays revealed that Bf66946 binds to the surface of Gram-positive bacteria Staphylococcus aureus and Streptococcus pneumonia via a couple of acidic residues at the concave. In addition, the closest homolog of Bf66946 is highly expressed in the potential immune organ gill of Branchiostoma belcheri. Altogether, our findings provide the first structural evidence for the emergence of VLR-like molecules in the basal chordates.

-	~~Authors:~~ Cao, ~~D.D.~~, Cheng, W., Jiang~~, Y.L.~~, Wang~~, W.J.~~, Li, Q., Chen, Y., Zhou~~, C~~.Z.	+	Structure of a variable lymphocyte receptor-like protein from the amphioxus Branchiostoma floridae.,Cao DD, Liao X, Cheng W, Jiang YL, Wang WJ, Li Q, Chen JY, Chen Y, Zhou CZ Sci Rep. 2016 Jan 29;6:19951. doi: 10.1038/srep19951. PMID:26821753<ref>PMID:26821753</ref>

-	~~Description: Structure of~~ a ~~variable lymphocyte receptor-like protein Bf66946 from Branchiostoma floridae~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Cao, D.D]]	+	<div class="pdbe-citations 4xsq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cao, D D]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]
-	[[Category: Jiang, Y.L]]
-	[[Category: Li, Q]]
-	[[Category: Wang, W.J]]
	[[Category: Cheng, W]]		[[Category: Cheng, W]]
-	[[Category: Zhou, C.Z]]	+	[[Category: Jiang, Y L]]
		+	[[Category: Li, Q]]
		+	[[Category: Wang, W J]]
		+	[[Category: Zhou, C Z]]
		+	[[Category: Amphioxus]]
		+	[[Category: Bf66946]]
		+	[[Category: Immune system]]
		+	[[Category: Leucine rich repeat]]
		+	[[Category: Variable lymphocyte receptor]]

OCA at 20:38, 9 March 2016

OCA — Wed, 09 Mar 2016 20:38:24 GMT

←Older revision		Revision as of 20:38, 9 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xsq is ON HOLD ~~until Paper Publication~~	+	The entry 4xsq is ON HOLD

	Authors: Cao, D.D., Cheng, W., Jiang, Y.L., Wang, W.J., Li, Q., Chen, Y., Zhou, C.Z.		Authors: Cao, D.D., Cheng, W., Jiang, Y.L., Wang, W.J., Li, Q., Chen, Y., Zhou, C.Z.

OCA at 23:19, 30 November 2015

OCA — Mon, 30 Nov 2015 23:19:12 GMT

←Older revision		Revision as of 23:19, 30 November 2015
Line 9:		Line 9:
	[[Category: Cao, D.D]]		[[Category: Cao, D.D]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]
-	[[Category: Wang, W.J]]
-	[[Category: Zhou, C.Z]]
	[[Category: Jiang, Y.L]]		[[Category: Jiang, Y.L]]
	[[Category: Li, Q]]		[[Category: Li, Q]]
		+	[[Category: Wang, W.J]]
	[[Category: Cheng, W]]		[[Category: Cheng, W]]
		+	[[Category: Zhou, C.Z]]

OCA at 09:47, 4 March 2015

OCA — Wed, 04 Mar 2015 09:47:10 GMT

←Older revision		Revision as of 09:47, 4 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xsq is ON HOLD	+	The entry 4xsq is ON HOLD until Paper Publication

	Authors: Cao, D.D., Cheng, W., Jiang, Y.L., Wang, W.J., Li, Q., Chen, Y., Zhou, C.Z.		Authors: Cao, D.D., Cheng, W., Jiang, Y.L., Wang, W.J., Li, Q., Chen, Y., Zhou, C.Z.

OCA at 11:39, 18 February 2015

OCA — Wed, 18 Feb 2015 11:39:08 GMT

←Older revision		Revision as of 11:39, 18 February 2015
Line 3:		Line 3:
	The entry 4xsq is ON HOLD		The entry 4xsq is ON HOLD

-	Authors: ~~Dong-Dong~~ Cao, ~~Wang~~ Cheng, ~~Yong-Liang~~ Jiang, ~~Wen-Jie~~ Wang, ~~Qiong~~ Li, ~~Yuxing~~ Chen, ~~Cong-Zhao~~ Zhou	+	Authors: Cao, D.D., Cheng, W., Jiang, Y.L., Wang, W.J., Li, Q., Chen, Y., Zhou, C.Z.

-	Description: Structure of a ~~putative~~ variable lymphocyte receptor Bf66946~~/VLRC1~~	+	Description: Structure of a variable lymphocyte receptor-like protein Bf66946 from Branchiostoma floridae
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Dong-Dong~~ Cao, Wang ~~Cheng~~, ~~Yong-Liang~~ Jiang, ~~Wen-Jie Wang, Qiong~~ Li, ~~Yuxing Chen~~, ~~Cong-Zhao Zhou~~]]	+	[[Category: Cao, D.D]]
		+	[[Category: Chen, Y]]
		+	[[Category: Wang, W.J]]
		+	[[Category: Zhou, C.Z]]
		+	[[Category: Jiang, Y.L]]
		+	[[Category: Li, Q]]
		+	[[Category: Cheng, W]]

OCA: Protected "4xsq" [edit=sysop:move=sysop]

OCA — Wed, 28 Jan 2015 15:48:13 GMT

Protected "4xsq" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:48, 28 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xsq is ON HOLD Authors: Dong-Dong Cao, Wang Cheng, Yong-Liang Jiang, Wen-Jie Wang, Qiong Li, Yuxing Chen, Cong-Zhao Zhou Description: Structure of...

OCA — Wed, 28 Jan 2015 15:48:12 GMT

New page: '''Unreleased structure''' The entry 4xsq is ON HOLD Authors: Dong-Dong Cao, Wang Cheng, Yong-Liang Jiang, Wen-Jie Wang, Qiong Li, Yuxing Chen, Cong-Zhao Zhou Description: Structure of...

New page

'''Unreleased structure'''

The entry 4xsq is ON HOLD

Authors: Dong-Dong Cao, Wang Cheng, Yong-Liang Jiang, Wen-Jie Wang, Qiong Li, Yuxing Chen, Cong-Zhao Zhou

Description: Structure of a putative variable lymphocyte receptor Bf66946/VLRC1
[[Category: Unreleased Structures]]
[[Category: Dong-Dong Cao, Wang Cheng, Yong-Liang Jiang, Wen-Jie Wang, Qiong Li, Yuxing Chen, Cong-Zhao Zhou]]