5ovw - Revision history

OCA at 01:26, 28 December 2023

OCA — Thu, 28 Dec 2023 01:26:03 GMT

←Older revision		Revision as of 01:26, 28 December 2023
Line 3:		Line 3:
	<StructureSection load='5ovw' size='340' side='right'caption='[[5ovw]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='5ovw' size='340' side='right'caption='[[5ovw]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ovw]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~] and [~~http~~://en.wikipedia.org/wiki/~~Camelus_glama Camelus~~ glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OVW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OVW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ovw]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OVW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OVW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</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]] 2.653Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>btuF, yadT, b0158, JW0154 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])~~</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ovw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ovw OCA], [~~http~~://pdbe.org/5ovw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ovw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ovw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ovw 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=5ovw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ovw OCA], [https://pdbe.org/5ovw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ovw RCSB], [https://www.ebi.ac.uk/pdbsum/5ovw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ovw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BTUF_ECOLI BTUF_ECOLI]] Part of the ABC transporter complex BtuCDF involved in vitamin B12 import. Binds vitamin B12 and delivers it to the periplasmic surface of BtuC.<ref>PMID:11790740</ref>	+	[https://www.uniprot.org/uniprot/BTUF_ECOLI BTUF_ECOLI] Part of the ABC transporter complex BtuCDF involved in vitamin B12 import. Binds vitamin B12 and delivers it to the periplasmic surface of BtuC.<ref>PMID:11790740</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
-	[[Category: ~~Camelus~~ glama]]	+	[[Category: Lama glama]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Glockshuber, R]]	+	[[Category: Glockshuber R]]
-	[[Category: Locher~~, K P~~]]	+	[[Category: Locher KP]]
-	[[Category: Mireku~~, S A~~]]	+	[[Category: Mireku SA]]
-	[[Category: Sauer~~, M M]]~~	+	[[Category: Sauer MM]]
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Nanobody]]~~	+
-	~~[[Category: Substrate-binding protein]]~~	+
-	~~[[Category: Transport protein]]~~	+
-	~~[[Category: Vitamin b12~~]]	+

OCA at 06:58, 16 October 2019

OCA — Wed, 16 Oct 2019 06:58:52 GMT

←Older revision		Revision as of 06:58, 16 October 2019
Line 1:		Line 1:

	==Nanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli==		==Nanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli==
-	<StructureSection load='5ovw' size='340' side='right' caption='[[5ovw]], [[Resolution\|resolution]] 2.65Å' scene=''>	+	<StructureSection load='5ovw' size='340' side='right'caption='[[5ovw]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ovw]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OVW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OVW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ovw]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Camelus_glama Camelus glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OVW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OVW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">btuF, yadT, b0158, JW0154 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=5ovw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ovw OCA], [http://pdbe.org/5ovw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ovw RCSB], [http://www.ebi.ac.uk/pdbsum/5ovw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ovw ProSAT]</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=5ovw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ovw OCA], [http://pdbe.org/5ovw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ovw RCSB], [http://www.ebi.ac.uk/pdbsum/5ovw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ovw ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Camelus glama]]
		+	[[Category: Large Structures]]
	[[Category: Glockshuber, R]]		[[Category: Glockshuber, R]]
	[[Category: Locher, K P]]		[[Category: Locher, K P]]

OCA at 07:40, 8 November 2017

OCA — Wed, 08 Nov 2017 07:40:20 GMT

←Older revision		Revision as of 07:40, 8 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ovw is ~~ON HOLD~~	+	==Nanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli==
		+	<StructureSection load='5ovw' size='340' side='right' caption='[[5ovw]], [[Resolution\|resolution]] 2.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ovw]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OVW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OVW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ovw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ovw OCA], [http://pdbe.org/5ovw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ovw RCSB], [http://www.ebi.ac.uk/pdbsum/5ovw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ovw ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BTUF_ECOLI BTUF_ECOLI]] Part of the ABC transporter complex BtuCDF involved in vitamin B12 import. Binds vitamin B12 and delivers it to the periplasmic surface of BtuC.<ref>PMID:11790740</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial ABC importers catalyze the uptake of essential nutrients including transition metals and metal-containing co-factors. Recently, an IgG antibody targeting the external binding protein of the Staphylococcus aureus Mn(II) ABC importer was reported to inhibit transport activity and reduce bacterial cell growth. We here explored the possibility of using alpaca-derived nanobodies to inhibit the vitamin B12 transporter of Escherichia coli, BtuCD-F, as a model system by generating nanobodies against the periplasmic binding protein BtuF. We isolated six nanobodies that competed with B12 for binding to BtuF, with inhibition constants between 10-6 and 10-9 M. Kinetic characterization of the nanobody-BtuF interactions revealed dissociation half-lives between 1.6 and 6 minutes and fast association rates between 104 and 106 M-1s-1. For the tightest-binding nanobody, we observed a reduction of in vitro transport activity of BtuCD-F when an excess of nanobody over B12 was used. The structure of BtuF in complex with the most effective nanobody Nb9 revealed the molecular basis of its inhibitory function. The CDR3 loop of Nb9 reached into the substrate-binding pocket of BtuF, preventing both B12 binding and BtuCD-F complex formation. Our results suggest that nanobodies can mediate ABC importer inhibition, providing an opportunity for novel antibiotic strategies.

-	~~Authors: Mireku~~, ~~S.A~~., Sauer~~, M.M.~~, Glockshuber, R., Locher~~, K~~.P.	+	Structural basis of nanobody-mediated blocking of BtuF, the cognate substrate-binding protein of the Escherichia coli vitamin B12 transporter BtuCD.,Mireku SA, Sauer MM, Glockshuber R, Locher KP Sci Rep. 2017 Oct 30;7(1):14296. doi: 10.1038/s41598-017-14512-8. PMID:29084999<ref>PMID:29084999</ref>

-	~~Description: Nanobody-bound BtuF~~, the ~~vitamin B12 binding protein in Escherichia coli~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Sauer, M.M]]~~	+	<div class="pdbe-citations 5ovw" style="background-color:#fffaf0;"></div>
-	~~[[Category: Locher, K.P]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Glockshuber, R]]		[[Category: Glockshuber, R]]
-	[[Category: Mireku, S.A]]	+	[[Category: Locher, K P]]
		+	[[Category: Mireku, S A]]
		+	[[Category: Sauer, M M]]
		+	[[Category: Inhibitor]]
		+	[[Category: Nanobody]]
		+	[[Category: Substrate-binding protein]]
		+	[[Category: Transport protein]]
		+	[[Category: Vitamin b12]]

OCA: Protected "5ovw" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:54:31 GMT

Protected "5ovw" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:54, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ovw is ON HOLD Authors: Mireku, S.A., Sauer, M.M., Glockshuber, R., Locher, K.P. Description: Nanobody-bound BtuF, the vitamin B12 binding protein...

OCA — Wed, 27 Sep 2017 12:54:30 GMT

New page: '''Unreleased structure''' The entry 5ovw is ON HOLD Authors: Mireku, S.A., Sauer, M.M., Glockshuber, R., Locher, K.P. Description: Nanobody-bound BtuF, the vitamin B12 binding protein...

New page

'''Unreleased structure'''

The entry 5ovw is ON HOLD

Authors: Mireku, S.A., Sauer, M.M., Glockshuber, R., Locher, K.P.

Description: Nanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli
[[Category: Unreleased Structures]]
[[Category: Sauer, M.M]]
[[Category: Locher, K.P]]
[[Category: Glockshuber, R]]
[[Category: Mireku, S.A]]