5m13 - Revision history

OCA at 18:19, 1 November 2023

2023-11-01T18:19:41Z

←Older revision		Revision as of 18:19, 1 November 2023
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	<StructureSection load='5m13' size='340' side='right'caption='[[5m13]], [[Resolution\|resolution]] 1.37Å' scene=''>		<StructureSection load='5m13' size='340' side='right'caption='[[5m13]], [[Resolution\|resolution]] 1.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m13]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~] and [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M13 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5M13 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m13]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M13 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M13 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>~~</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]] 1.372Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~malE, b4034, JW3994 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=83333 ECOLI])~~</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></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=5m13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m13 OCA], [~~http~~://pdbe.org/5m13 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5m13 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5m13 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5m13 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=5m13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m13 OCA], [https://pdbe.org/5m13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m13 RCSB], [https://www.ebi.ac.uk/pdbsum/5m13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m13 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI]] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.	+	[https://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Maltose-binding protein\|Maltose-binding protein]]	+	*[[Maltose-binding protein 3D structures\|Maltose-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Egloff, P]]	+	[[Category: Egloff P]]
-	[[Category: Seeger~~, M A~~]]	+	[[Category: Seeger MA]]
-	[[Category: Zimmermann, I]]	+	[[Category: Zimmermann I]]
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Maltose binding protein]]~~	+
-	~~[[Category: Nanobody]]~~	+
-	~~[[Category: Synthetic library~~]]	+

OCA at 06:33, 16 October 2019

2019-10-16T06:33:10Z

←Older revision		Revision as of 06:33, 16 October 2019
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	==Synthetic nanobody in complex with MBP==		==Synthetic nanobody in complex with MBP==
-	<StructureSection load='5m13' size='340' side='right' caption='[[5m13]], [[Resolution\|resolution]] 1.37Å' scene=''>	+	<StructureSection load='5m13' size='340' side='right'caption='[[5m13]], [[Resolution\|resolution]] 1.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5m13]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M13 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M13 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5m13]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M13 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M13 FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Egloff, P]]		[[Category: Egloff, P]]

OCA at 20:42, 2 December 2018

2018-12-02T20:42:35Z

←Older revision		Revision as of 20:42, 2 December 2018
Line 3:		Line 3:
	<StructureSection load='5m13' size='340' side='right' caption='[[5m13]], [[Resolution\|resolution]] 1.37Å' scene=''>		<StructureSection load='5m13' size='340' side='right' caption='[[5m13]], [[Resolution\|resolution]] 1.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m13]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M13 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M13 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m13]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M13 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M13 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></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></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">malE, b4034, JW3994 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=5m13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m13 OCA], [http://pdbe.org/5m13 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m13 RCSB], [http://www.ebi.ac.uk/pdbsum/5m13 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m13 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=5m13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m13 OCA], [http://pdbe.org/5m13 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m13 RCSB], [http://www.ebi.ac.uk/pdbsum/5m13 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m13 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI]] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.		[[http://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI]] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mechanistic and structural studies of membrane proteins require their stabilization in specific conformations. Single domain antibodies are potent reagents for this purpose, but their generation relies on immunizations, which impedes selections in the presence of ligands typically needed to populate defined conformational states. To overcome this key limitation, we developed an in vitro selection platform based on synthetic single domain antibodies named sybodies. To target the limited hydrophilic surfaces of membrane proteins, we designed three sybody libraries that exhibit different shapes and moderate hydrophobicity of the randomized surface. A robust binder selection cascade combining ribosome and phage display enabled the generation of conformation-selective, high affinity sybodies against an ABC transporter and two previously intractable human SLC transporters, GlyT1 and ENT1. The platform does not require access to animal facilities and builds exclusively on commercially available reagents, thus enabling every lab to rapidly generate binders against challenging membrane proteins.
		+
		+	Synthetic single domain antibodies for the conformational trapping of membrane proteins.,Zimmermann I, Egloff P, Hutter CA, Arnold FM, Stohler P, Bocquet N, Hug MN, Huber S, Siegrist M, Hetemann L, Gera J, Gmur S, Spies P, Gygax D, Geertsma ER, Dawson RJ, Seeger MA Elife. 2018 May 24;7. pii: 34317. doi: 10.7554/eLife.34317. PMID:29792401<ref>PMID:29792401</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5m13" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Maltose-binding protein\|Maltose-binding protein]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
		+	[[Category: Synthetic construct sequences]]
	[[Category: Egloff, P]]		[[Category: Egloff, P]]
	[[Category: Seeger, M A]]		[[Category: Seeger, M A]]

OCA at 07:24, 15 November 2017

2017-11-15T07:24:42Z

←Older revision		Revision as of 07:24, 15 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5m13 is ~~ON HOLD~~	+	==Synthetic nanobody in complex with MBP==
-		+	<StructureSection load='5m13' size='340' side='right' caption='[[5m13]], [[Resolution\|resolution]] 1.37Å' scene=''>
-	~~Authors~~: ~~Zimmermann~~, I., ~~Egloff~~, P., ~~Seeger~~, M.A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5m13]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M13 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M13 FirstGlance]. <br>
-	~~Description: Synthetic nanobody in complex with MBP~~	+	</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></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5m13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m13 OCA], [http://pdbe.org/5m13 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m13 RCSB], [http://www.ebi.ac.uk/pdbsum/5m13 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m13 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI]] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides.
		+	__TOC__
		+	</StructureSection>
	[[Category: Egloff, P]]		[[Category: Egloff, P]]
-	[[Category: Seeger, M.A]]	+	[[Category: Seeger, M A]]
	[[Category: Zimmermann, I]]		[[Category: Zimmermann, I]]
		+	[[Category: Immune system]]
		+	[[Category: Maltose binding protein]]
		+	[[Category: Nanobody]]
		+	[[Category: Synthetic library]]

OCA at 10:59, 9 March 2017

2017-03-09T10:59:11Z

←Older revision		Revision as of 10:59, 9 March 2017
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	Description: Synthetic nanobody in complex with MBP		Description: Synthetic nanobody in complex with MBP
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Seeger, M.A]]
	[[Category: Egloff, P]]		[[Category: Egloff, P]]
		+	[[Category: Seeger, M.A]]
	[[Category: Zimmermann, I]]		[[Category: Zimmermann, I]]

OCA: Protected "5m13" [edit=sysop:move=sysop]

2016-10-19T15:02:21Z

Protected "5m13" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:02, 19 October 2016

OCA: New page: '''Unreleased structure''' The entry 5m13 is ON HOLD Authors: Zimmermann, I., Egloff, P., Seeger, M.A. Description: Synthetic nanobody in complex with MBP [[Category: Unreleased Struct...

2016-10-19T15:02:20Z

New page: '''Unreleased structure''' The entry 5m13 is ON HOLD Authors: Zimmermann, I., Egloff, P., Seeger, M.A. Description: Synthetic nanobody in complex with MBP [[Category: Unreleased Struct...

New page

'''Unreleased structure'''

The entry 5m13 is ON HOLD

Authors: Zimmermann, I., Egloff, P., Seeger, M.A.

Description: Synthetic nanobody in complex with MBP
[[Category: Unreleased Structures]]
[[Category: Seeger, M.A]]
[[Category: Egloff, P]]
[[Category: Zimmermann, I]]