2o6d - Revision history

OCA at 06:28, 3 April 2024

OCA — Wed, 03 Apr 2024 06:28:53 GMT

←Older revision		Revision as of 06:28, 3 April 2024
Line 20:		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=2o6d 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=2o6d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The Tp34 (TP0971) membrane lipoprotein of Treponema pallidum, an obligate human pathogen and the agent of syphilis, was previously reported to have lactoferrin binding properties. Given the non-cultivatable nature of T. pallidum, a structure-to-function approach was pursued to clarify further potential relationships between the Tp34 structural and biochemical properties and its propensity to bind human lactoferrin. The crystal structure of a nonacylated, recombinant form of Tp34 (rTp34), solved to a resolution of 1.9A(,) revealed two metaloccupied binding sites within a dimer; the identity of the ion most likely was zinc. Residues from both of the monomers contributed to the interfacial metal-binding sites; a novel feature was that the delta-sulfur of methionine coordinated the zinc ion. Analytical ultracentrifugation showed that, in solution, rTp34 formed a metal-stabilized dimer and that rTp34 bound human lactoferrin with a stoichiometry of 2:1. Isothermal titration calorimetry further revealed that rTp34 bound human lactoferrin at high (submicromolar) affinity. Finally, membrane topology studies revealed that native Tp34 is not located on the outer surface (outer membrane) of T. pallidum but, rather, is periplasmic. How propensity of Tp34 to bind zinc and the iron-sequestering lactoferrin may relate overall to the biology of T. pallidum infection in humans is discussed.
-
-	Crystal structure of the Tp34 (TP0971) lipoprotein of treponema pallidum: implications of its metal-bound state and affinity for human lactoferrin.,Deka RK, Brautigam CA, Tomson FL, Lumpkins SB, Tomchick DR, Machius M, Norgard MV J Biol Chem. 2007 Feb 23;282(8):5944-58. Epub 2006 Dec 27. PMID:17192261<ref>PMID:17192261</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2o6d" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 00:15, 28 December 2023

OCA — Thu, 28 Dec 2023 00:15:01 GMT

←Older revision		Revision as of 00:15, 28 December 2023
Line 3:		Line 3:
	<StructureSection load='2o6d' size='340' side='right'caption='[[2o6d]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='2o6d' size='340' side='right'caption='[[2o6d]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2o6d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"microspironema_pallidum"_(schaudinn_and_hoffmann_1905)_stiles_and_pfender_1905 "microspironema~~ pallidum~~" (schaudinn and hoffmann 1905) stiles and pfender 1905~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O6D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2o6d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Treponema_pallidum Treponema pallidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O6D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.86Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2o6c\|2o6c]], [[2o6e\|2o6e]], [[2o6f\|2o6f]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tpd ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160 "Microspironema pallidum" (Schaudinn and Hoffmann 1905) Stiles and Pfender 1905])</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=2o6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6d OCA], [https://pdbe.org/2o6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o6d RCSB], [https://www.ebi.ac.uk/pdbsum/2o6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o6d 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=2o6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6d OCA], [https://pdbe.org/2o6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o6d RCSB], [https://www.ebi.ac.uk/pdbsum/2o6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o6d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TA34_TREPA TA34_TREPA]] This antigen is a pathogen-specific membrane immunogen.	+	[https://www.uniprot.org/uniprot/TA34_TREPA TA34_TREPA] This antigen is a pathogen-specific membrane immunogen.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Brautigam, C A~~]]	+	[[Category: Treponema pallidum]]
-	[[Category: ~~Deka, R K~~]]	+	[[Category: Brautigam CA]]
-	[[Category: ~~Lumpkins, S B~~]]	+	[[Category: Deka RK]]
-	[[Category: ~~Machius, M~~]]	+	[[Category: Lumpkins SB]]
-	[[Category: ~~Norgard,~~ M V]]	+	[[Category: Machius M]]
-	[[Category: ~~Tomchick, D R~~]]	+	[[Category: Norgard MV]]
-	[[Category: ~~Dimer]]~~	+	[[Category: Tomchick DR]]
-	~~[[Category: Ig-fold]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Metal-ion binding]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Syphili~~]]	+

OCA at 16:01, 8 June 2021

OCA — Tue, 08 Jun 2021 16:01:21 GMT

←Older revision		Revision as of 16:01, 8 June 2021
Line 1:		Line 1:

	==Structure of native rTp34 from Treponema pallidum==		==Structure of native rTp34 from Treponema pallidum==
-	<StructureSection load='2o6d' size='340' side='right' caption='[[2o6d]], [[Resolution\|resolution]] 1.86Å' scene=''>	+	<StructureSection load='2o6d' size='340' side='right'caption='[[2o6d]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2o6d]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"microspironema_pallidum"_(schaudinn_and_hoffmann_1905)_stiles_and_pfender_1905 "microspironema pallidum" (schaudinn and hoffmann 1905) stiles and pfender 1905]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2O6D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2o6d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"microspironema_pallidum"_(schaudinn_and_hoffmann_1905)_stiles_and_pfender_1905 "microspironema pallidum" (schaudinn and hoffmann 1905) stiles and pfender 1905]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O6D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o6c\|2o6c]], [[2o6e\|2o6e]], [[2o6f\|2o6f]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2o6c\|2o6c]], [[2o6e\|2o6e]], [[2o6f\|2o6f]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tpd ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160 "Microspironema pallidum" (Schaudinn and Hoffmann 1905) Stiles and Pfender 1905])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tpd ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160 "Microspironema pallidum" (Schaudinn and Hoffmann 1905) Stiles and Pfender 1905])</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=2o6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6d OCA], [~~http~~://pdbe.org/2o6d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2o6d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2o6d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2o6d 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=2o6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6d OCA], [https://pdbe.org/2o6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o6d RCSB], [https://www.ebi.ac.uk/pdbsum/2o6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o6d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TA34_TREPA TA34_TREPA]] This antigen is a pathogen-specific membrane immunogen.	+	[[https://www.uniprot.org/uniprot/TA34_TREPA TA34_TREPA]] This antigen is a pathogen-specific membrane immunogen.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Brautigam, C A]]		[[Category: Brautigam, C A]]
	[[Category: Deka, R K]]		[[Category: Deka, R K]]

OCA at 07:35, 22 August 2018

OCA — Wed, 22 Aug 2018 07:35:01 GMT

←Older revision		Revision as of 07:35, 22 August 2018
Line 1:		Line 1:
		+
	==Structure of native rTp34 from Treponema pallidum==		==Structure of native rTp34 from Treponema pallidum==
	<StructureSection load='2o6d' size='340' side='right' caption='[[2o6d]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='2o6d' size='340' side='right' caption='[[2o6d]], [[Resolution\|resolution]] 1.86Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o6c\|2o6c]], [[2o6e\|2o6e]], [[2o6f\|2o6f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o6c\|2o6c]], [[2o6e\|2o6e]], [[2o6f\|2o6f]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tpd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160 "Microspironema pallidum" (Schaudinn and Hoffmann 1905) Stiles and Pfender 1905])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tpd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160 "Microspironema pallidum" (Schaudinn and Hoffmann 1905) Stiles and Pfender 1905])</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=2o6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6d OCA], [http://pdbe.org/2o6d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o6d RCSB], [http://www.ebi.ac.uk/pdbsum/2o6d 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=2o6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6d OCA], [http://pdbe.org/2o6d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o6d RCSB], [http://www.ebi.ac.uk/pdbsum/2o6d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2o6d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o6/2o6d_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o6/2o6d_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>
	</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=2o6d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:32, 11 September 2015

OCA — Fri, 11 Sep 2015 23:32:41 GMT

←Older revision		Revision as of 23:32, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2o6d' size='340' side='right' caption='[[2o6d]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='2o6d' size='340' side='right' caption='[[2o6d]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2o6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Treponema_pallidum Treponema~~ pallidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O6D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2o6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"microspironema_pallidum"_(schaudinn_and_hoffmann_1905)_stiles_and_pfender_1905 "microspironema pallidum" (schaudinn and hoffmann 1905) stiles and pfender 1905]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O6D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o6c\|2o6c]], [[2o6e\|2o6e]], [[2o6f\|2o6f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o6c\|2o6c]], [[2o6e\|2o6e]], [[2o6f\|2o6f]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tpd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160 ~~Treponema~~ pallidum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tpd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160 "Microspironema pallidum" (Schaudinn and Hoffmann 1905) Stiles and Pfender 1905])</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=2o6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o6d RCSB], [http://www.ebi.ac.uk/pdbsum/2o6d 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=2o6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6d OCA], [http://pdbe.org/2o6d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o6d RCSB], [http://www.ebi.ac.uk/pdbsum/2o6d PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2o6d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Treponema pallidum]]
	[[Category: Brautigam, C A]]		[[Category: Brautigam, C A]]
	[[Category: Deka, R K]]		[[Category: Deka, R K]]

OCA at 20:52, 25 December 2014

OCA — Thu, 25 Dec 2014 20:52:37 GMT

←Older revision		Revision as of 20:52, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2o6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Treponema_pallidum Treponema pallidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O6D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2o6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Treponema_pallidum Treponema pallidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O6D FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o6c\|2o6c]], [[2o6e\|2o6e]], [[2o6f\|2o6f]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o6c\|2o6c]], [[2o6e\|2o6e]], [[2o6f\|2o6f]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tpd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160 Treponema pallidum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tpd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160 Treponema pallidum])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2o6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o6d RCSB], [http://www.ebi.ac.uk/pdbsum/2o6d 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=2o6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o6d RCSB], [http://www.ebi.ac.uk/pdbsum/2o6d PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TA34_TREPA TA34_TREPA]] This antigen is a pathogen-specific membrane immunogen.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Treponema pallidum]]		[[Category: Treponema pallidum]]
-	[[Category: Brautigam, C A.]]	+	[[Category: Brautigam, C A]]
-	[[Category: Deka, R K.]]	+	[[Category: Deka, R K]]
-	[[Category: Lumpkins, S B.]]	+	[[Category: Lumpkins, S B]]
-	[[Category: Machius, M.]]	+	[[Category: Machius, M]]
-	[[Category: Norgard, M V.]]	+	[[Category: Norgard, M V]]
-	[[Category: Tomchick, D R.]]	+	[[Category: Tomchick, D R]]
	[[Category: Dimer]]		[[Category: Dimer]]
	[[Category: Ig-fold]]		[[Category: Ig-fold]]

OCA at 20:23, 30 September 2014

OCA — Tue, 30 Sep 2014 20:23:01 GMT

←Older revision		Revision as of 20:23, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2o6d.~~png~~\|~~left~~\|200px]]	+	==Structure of native rTp34 from Treponema pallidum==
		+	<StructureSection load='2o6d' size='340' side='right' caption='[[2o6d]], [[Resolution\|resolution]] 1.86Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2o6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Treponema_pallidum Treponema pallidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2O6D FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2o6c\|2o6c]], [[2o6e\|2o6e]], [[2o6f\|2o6f]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tpd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160 Treponema pallidum])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2o6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o6d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2o6d RCSB], [http://www.ebi.ac.uk/pdbsum/2o6d 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/o6/2o6d_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 ==
		+	The Tp34 (TP0971) membrane lipoprotein of Treponema pallidum, an obligate human pathogen and the agent of syphilis, was previously reported to have lactoferrin binding properties. Given the non-cultivatable nature of T. pallidum, a structure-to-function approach was pursued to clarify further potential relationships between the Tp34 structural and biochemical properties and its propensity to bind human lactoferrin. The crystal structure of a nonacylated, recombinant form of Tp34 (rTp34), solved to a resolution of 1.9A(,) revealed two metaloccupied binding sites within a dimer; the identity of the ion most likely was zinc. Residues from both of the monomers contributed to the interfacial metal-binding sites; a novel feature was that the delta-sulfur of methionine coordinated the zinc ion. Analytical ultracentrifugation showed that, in solution, rTp34 formed a metal-stabilized dimer and that rTp34 bound human lactoferrin with a stoichiometry of 2:1. Isothermal titration calorimetry further revealed that rTp34 bound human lactoferrin at high (submicromolar) affinity. Finally, membrane topology studies revealed that native Tp34 is not located on the outer surface (outer membrane) of T. pallidum but, rather, is periplasmic. How propensity of Tp34 to bind zinc and the iron-sequestering lactoferrin may relate overall to the biology of T. pallidum infection in humans is discussed.

-	~~{{STRUCTURE_2o6d\| PDB=2o6d \| SCENE= }}~~	+	Crystal structure of the Tp34 (TP0971) lipoprotein of treponema pallidum: implications of its metal-bound state and affinity for human lactoferrin.,Deka RK, Brautigam CA, Tomson FL, Lumpkins SB, Tomchick DR, Machius M, Norgard MV J Biol Chem. 2007 Feb 23;282(8):5944-58. Epub 2006 Dec 27. PMID:17192261<ref>PMID:17192261</ref>

-	~~===Structure~~ of ~~native rTp34 from Treponema pallidum===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17192261}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2o6d]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Treponema_pallidum Treponema pallidum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2O6D OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017192261<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Treponema pallidum]]		[[Category: Treponema pallidum]]
	[[Category: Brautigam, C A.]]		[[Category: Brautigam, C A.]]

OCA: Protected "2o6d" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 12:46:29 GMT

Protected "2o6d" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:46, 7 January 2013

OCA at 12:46, 7 January 2013

OCA — Mon, 07 Jan 2013 12:46:26 GMT

←Older revision		Revision as of 12:46, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2o6d.png\|left\|200px]]		[[Image:2o6d.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2o6d", 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_2o6d\| PDB=2o6d \| SCENE= }}		{{STRUCTURE_2o6d\| PDB=2o6d \| SCENE= }}

	===Structure of native rTp34 from Treponema pallidum===		===Structure of native rTp34 from Treponema pallidum===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17192261}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17192261 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17192261}}		{{ABSTRACT_PUBMED_17192261}}

	==About this Structure==		==About this Structure==
-	~~2O6D~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Treponema_pallidum Treponema pallidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6D OCA].	+	[[2o6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Treponema_pallidum Treponema pallidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6D OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17192261~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017192261</ref><references group="xtra"/>
	[[Category: Treponema pallidum]]		[[Category: Treponema pallidum]]
	[[Category: Brautigam, C A.]]		[[Category: Brautigam, C A.]]
Line 33:		Line 21:
	[[Category: Dimer]]		[[Category: Dimer]]
	[[Category: Ig-fold]]		[[Category: Ig-fold]]
		+	[[Category: Membrane protein]]
	[[Category: Metal-ion binding]]		[[Category: Metal-ion binding]]
		+	[[Category: Protein binding]]
	[[Category: Syphili]]		[[Category: Syphili]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 06:53:02 2009''

OCA at 04:53, 18 February 2009

OCA — Wed, 18 Feb 2009 04:53:04 GMT

←Older revision		Revision as of 04:53, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2O6D is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Treponema_pallidum Treponema pallidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6D OCA].	+	2O6D is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Treponema_pallidum Treponema pallidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O6D OCA].

	==Reference==		==Reference==
-	Crystal structure of the Tp34 (TP0971) lipoprotein of treponema pallidum: implications of its metal-bound state and affinity for human lactoferrin., Deka RK, Brautigam CA, Tomson FL, Lumpkins SB, Tomchick DR, Machius M, Norgard MV, J Biol Chem. 2007 Feb 23;282(8):5944-58. Epub 2006 Dec 27. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17192261 17192261]~~	+	<ref group="xtra">PMID:17192261</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Treponema pallidum]]		[[Category: Treponema pallidum]]
	[[Category: Brautigam, C A.]]		[[Category: Brautigam, C A.]]
Line 37:		Line 36:
	[[Category: Syphili]]		[[Category: Syphili]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 13~~:39:~~13 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 06:53:02 2009''