3tvy - Revision history

OCA at 10:15, 1 March 2024

OCA — Fri, 01 Mar 2024 10:15:08 GMT

←Older revision		Revision as of 10:15, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3tvy' size='340' side='right'caption='[[3tvy]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3tvy' size='340' side='right'caption='[[3tvy]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tvy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Streptococcus_agalactiae_(serotype_v)~~ Streptococcus agalactiae ~~(serotype v)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TVY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tvy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_agalactiae_serogroup_V Streptococcus agalactiae serogroup V]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TVY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EPE:4~~-(2~~-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3tw0\|3tw0]], [[3txa\|3txa]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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">SAG0649 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216466 Streptococcus agalactiae (serotype V)])~~</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=3tvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvy OCA], [https://pdbe.org/3tvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tvy RCSB], [https://www.ebi.ac.uk/pdbsum/3tvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tvy 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=3tvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvy OCA], [https://pdbe.org/3tvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tvy RCSB], [https://www.ebi.ac.uk/pdbsum/3tvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tvy ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q8E0S5_STRA5 Q8E0S5_STRA5]
-	~~The crystal structure of a 75 kDa central fragment of GBS104, a tip pilin from the 2063V~~/R strain of Streptococcus agalactiae (group B streptococcus; GBS), is reported. In addition, a homology model of the remaining two domains of GBS104 was built and a model of full-length GBS104 was generated by combining the homology model (the N1 and N4 domains) and the crystal structure of the 75 kDa fragment (the N2 and N3 domains). This rod-shaped GBS104 model is constructed of three IgG-like domains (the N1, N2 and N4 domains) and one vWFA-like domain (the N3 domain). The N1 and N2 domains of GBS104 are assembled with distinct and remote segments contributed by the N- and C-termini. The metal-binding site in the N3 domain of GBS104 is in the closed/~~low-affinity conformation~~. ~~Interestingly, this domain hosts two long arms that project away from the metal-binding site~~. ~~Using site-directed mutagenesis, two cysteine residues that lock the N3 domain of GBS104 into the open~~/high-affinity conformation were introduced. Both wild-type and disulfide-locked recombinant proteins were tested for binding to extracellular matrix proteins such as collagen, fibronectin, fibrinogen and laminin, and an increase in fibronectin binding affinity was identified for the disulfide-locked N3 domain, suggesting that induced conformational changes may play a possible role in receptor binding.	+

-	Structure of Streptococcus agalactiae tip pilin GBS104: a model for GBS pili assembly and host interactions.,Krishnan V, Dwivedi P, Kim BJ, Samal A, Macon K, Ma X, Mishra A, Doran KS, Ton-That H, Narayana SV Acta Crystallogr D Biol Crystallogr. 2013 Jun;69(Pt 6):1073-89. doi:, 10.1107/S0907444913004642. Epub 2013 May 15. PMID:23695252<ref>PMID:23695252</ref>	+	==See Also==
-		+	*[[Pilin 3D structures\|Pilin 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3tvy" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Krishnan,~~ V]]	+	[[Category: Streptococcus agalactiae serogroup V]]
-	[[Category: ~~Narayana, S~~ V.L]]	+	[[Category: Krishnan V]]
-	[[Category: ~~Ancillary pilin]]~~	+	[[Category: Narayana SVL]]
-	~~[[Category: Cell adhesion]]~~	+
-	~~[[Category: Gram-positive bacterial cell surface]]~~	+
-	~~[[Category: Vwfa fold~~]]	+

OCA at 05:47, 13 July 2022

OCA — Wed, 13 Jul 2022 05:47:40 GMT

←Older revision		Revision as of 05:47, 13 July 2022
Line 1:		Line 1:

	==Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae==		==Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae==
-	<StructureSection load='3tvy' size='340' side='right' caption='[[3tvy]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3tvy' size='340' side='right'caption='[[3tvy]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tvy]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Streptococcus_agalactiae_(serotype_v) Streptococcus agalactiae (serotype v)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3TVY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tvy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_agalactiae_(serotype_v) Streptococcus agalactiae (serotype v)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TVY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tw0\|3tw0]], [[3txa\|3txa]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3tw0\|3tw0]], [[3txa\|3txa]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAG0649 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216466 Streptococcus agalactiae (serotype V)])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAG0649 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216466 Streptococcus agalactiae (serotype V)])</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=3tvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvy OCA], [~~http~~://pdbe.org/3tvy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3tvy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3tvy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3tvy 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=3tvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvy OCA], [https://pdbe.org/3tvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tvy RCSB], [https://www.ebi.ac.uk/pdbsum/3tvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tvy ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Krishnan, V]]		[[Category: Krishnan, V]]
	[[Category: Narayana, S V.L]]		[[Category: Narayana, S V.L]]

OCA at 02:47, 5 August 2016

OCA — Fri, 05 Aug 2016 02:47:10 GMT

←Older revision		Revision as of 02:47, 5 August 2016
Line 1:		Line 1:
-	{{STRUCTURE_3tvy\| PDB=3tvy \| SCENE= }}
-	===Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae===
-	{{ABSTRACT_PUBMED_23695252}}

-	==~~About this Structure~~==	+	==Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae==
-	[[3tvy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptococcus_agalactiae_serogroup_v~~ Streptococcus agalactiae ~~serogroup~~ v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVY OCA].	+	<StructureSection load='3tvy' size='340' side='right' caption='[[3tvy]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3tvy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_agalactiae_(serotype_v) Streptococcus agalactiae (serotype v)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TVY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3tw0\|3tw0]], [[3txa\|3txa]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAG0649 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216466 Streptococcus agalactiae (serotype V)])</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=3tvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvy OCA], [http://pdbe.org/3tvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tvy RCSB], [http://www.ebi.ac.uk/pdbsum/3tvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tvy ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of a 75 kDa central fragment of GBS104, a tip pilin from the 2063V/R strain of Streptococcus agalactiae (group B streptococcus; GBS), is reported. In addition, a homology model of the remaining two domains of GBS104 was built and a model of full-length GBS104 was generated by combining the homology model (the N1 and N4 domains) and the crystal structure of the 75 kDa fragment (the N2 and N3 domains). This rod-shaped GBS104 model is constructed of three IgG-like domains (the N1, N2 and N4 domains) and one vWFA-like domain (the N3 domain). The N1 and N2 domains of GBS104 are assembled with distinct and remote segments contributed by the N- and C-termini. The metal-binding site in the N3 domain of GBS104 is in the closed/low-affinity conformation. Interestingly, this domain hosts two long arms that project away from the metal-binding site. Using site-directed mutagenesis, two cysteine residues that lock the N3 domain of GBS104 into the open/high-affinity conformation were introduced. Both wild-type and disulfide-locked recombinant proteins were tested for binding to extracellular matrix proteins such as collagen, fibronectin, fibrinogen and laminin, and an increase in fibronectin binding affinity was identified for the disulfide-locked N3 domain, suggesting that induced conformational changes may play a possible role in receptor binding.

-	~~==Reference==~~	+	Structure of Streptococcus agalactiae tip pilin GBS104: a model for GBS pili assembly and host interactions.,Krishnan V, Dwivedi P, Kim BJ, Samal A, Macon K, Ma X, Mishra A, Doran KS, Ton-That H, Narayana SV Acta Crystallogr D Biol Crystallogr. 2013 Jun;69(Pt 6):1073-89. doi:, 10.1107/S0907444913004642. Epub 2013 May 15. PMID:23695252<ref>PMID:23695252</ref>
-	<ref ~~group="xtra"~~>PMID:~~023695252~~</ref><~~references group~~="~~xtra~~"/><references/>	+
-	~~[[Category: Streptococcus agalactiae serogroup v]]~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: Krishnan, V.]]	+	</div>
-	[[Category: Narayana, S V.L.]]	+	<div class="pdbe-citations 3tvy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Krishnan, V]]
		+	[[Category: Narayana, S V.L]]
	[[Category: Ancillary pilin]]		[[Category: Ancillary pilin]]
	[[Category: Cell adhesion]]		[[Category: Cell adhesion]]
	[[Category: Gram-positive bacterial cell surface]]		[[Category: Gram-positive bacterial cell surface]]
	[[Category: Vwfa fold]]		[[Category: Vwfa fold]]

OCA at 13:41, 19 June 2013

OCA — Wed, 19 Jun 2013 13:41:31 GMT

←Older revision		Revision as of 13:41, 19 June 2013
Line 1:		Line 1:
	{{STRUCTURE_3tvy\| PDB=3tvy \| SCENE= }}		{{STRUCTURE_3tvy\| PDB=3tvy \| SCENE= }}
	===Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae===		===Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae===
		+	{{ABSTRACT_PUBMED_23695252}}

	==About this Structure==		==About this Structure==
	[[3tvy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_agalactiae_serogroup_v Streptococcus agalactiae serogroup v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVY OCA].		[[3tvy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_agalactiae_serogroup_v Streptococcus agalactiae serogroup v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVY OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023695252</ref><references group="xtra"/><references/>
	[[Category: Streptococcus agalactiae serogroup v]]		[[Category: Streptococcus agalactiae serogroup v]]
	[[Category: Krishnan, V.]]		[[Category: Krishnan, V.]]

OCA at 08:52, 27 March 2013

OCA — Wed, 27 Mar 2013 08:52:38 GMT

←Older revision		Revision as of 08:52, 27 March 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_3tvy\| PDB=3tvy \| SCENE= }}
		+	===Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae===

-	~~The entry~~ 3tvy is ~~ON HOLD until Mar 27 2014~~	+	==About this Structure==
-		+	[[3tvy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_agalactiae_serogroup_v Streptococcus agalactiae serogroup v]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVY OCA].
-	~~Authors~~: Krishnan, V., Narayana, S.V.L.	+	[[Category: Streptococcus agalactiae serogroup v]]
-		+	[[Category: Krishnan, V.]]
-	~~Description~~: ~~Structural Analysis of Adhesive Tip~~ pilin~~, GBS104 from Group B Streptococcus agalactiae~~	+	[[Category: Narayana, S V.L.]]
		+	[[Category: Ancillary pilin]]
		+	[[Category: Cell adhesion]]
		+	[[Category: Gram-positive bacterial cell surface]]
		+	[[Category: Vwfa fold]]

OCA at 04:38, 5 September 2012

OCA — Wed, 05 Sep 2012 04:38:30 GMT

←Older revision		Revision as of 04:38, 5 September 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3tvy is ON HOLD until ~~Paper Publication~~	+	The entry 3tvy is ON HOLD until Mar 27 2014

	Authors: Krishnan, V., Narayana, S.V.L.		Authors: Krishnan, V., Narayana, S.V.L.

	Description: Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae		Description: Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae

OCA at 08:44, 30 October 2011

OCA — Sun, 30 Oct 2011 08:44:37 GMT

←Older revision		Revision as of 08:44, 30 October 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3tvy is ON HOLD	+	The entry 3tvy is ON HOLD until Paper Publication

	Authors: Krishnan, V., Narayana, S.V.L.		Authors: Krishnan, V., Narayana, S.V.L.

	Description: Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae		Description: Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae

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

OCA — Wed, 28 Sep 2011 05:18:43 GMT

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

←Older revision

Revision as of 05:18, 28 September 2011

OCA: New page: '''Unreleased structure''' The entry 3tvy is ON HOLD Authors: Krishnan, V., Narayana, S.V.L. Description: Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus a...

OCA — Wed, 28 Sep 2011 05:18:41 GMT

New page: '''Unreleased structure''' The entry 3tvy is ON HOLD Authors: Krishnan, V., Narayana, S.V.L. Description: Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus a...

New page

'''Unreleased structure'''

The entry 3tvy is ON HOLD

Authors: Krishnan, V., Narayana, S.V.L.

Description: Structural Analysis of Adhesive Tip pilin, GBS104 from Group B Streptococcus agalactiae