4x0k - Revision history

OCA at 07:39, 27 September 2023

OCA — Wed, 27 Sep 2023 07:39:43 GMT

←Older revision		Revision as of 07:39, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x0k]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X0K FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x0k]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X0K FirstGlance]. <br>
-	</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=4x0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0k OCA], [https://pdbe.org/4x0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x0k RCSB], [https://www.ebi.ac.uk/pdbsum/4x0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0k ProSAT]</span></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]] 2.04Å</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=4x0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0k OCA], [https://pdbe.org/4x0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x0k RCSB], [https://www.ebi.ac.uk/pdbsum/4x0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:05, 12 April 2023

OCA — Wed, 12 Apr 2023 21:05:55 GMT

←Older revision		Revision as of 21:05, 12 April 2023
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	<StructureSection load='4x0k' size='340' side='right'caption='[[4x0k]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='4x0k' size='340' side='right'caption='[[4x0k]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x0k]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4X0K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x0k]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X0K FirstGlance]. <br>
-	</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=4x0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0k OCA], [~~http~~://pdbe.org/4x0k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4x0k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4x0k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0k ProSAT]</span></td></tr>	+	</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=4x0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0k OCA], [https://pdbe.org/4x0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x0k RCSB], [https://www.ebi.ac.uk/pdbsum/4x0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Johnson~~, J L~~]]	+	[[Category: Johnson JL]]
-	[[Category: Lieberman~~, R L]]~~	+	[[Category: Lieberman RL]]
-	~~[[Category: Antibody fragment]]~~	+
-	~~[[Category: Crystallization chaperone]]~~	+
-	~~[[Category: Fab fragment]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 07:50, 4 March 2020

OCA — Wed, 04 Mar 2020 07:50:43 GMT

←Older revision		Revision as of 07:50, 4 March 2020
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	==Engineered Fab fragment specific for EYMPME (EE) peptide==		==Engineered Fab fragment specific for EYMPME (EE) peptide==
-	<StructureSection load='4x0k' size='340' side='right' caption='[[4x0k]], [[Resolution\|resolution]] 2.04Å' scene=''>	+	<StructureSection load='4x0k' size='340' side='right'caption='[[4x0k]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x0k]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X0K FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x0k]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X0K FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Johnson, J L]]		[[Category: Johnson, J L]]
	[[Category: Lieberman, R L]]		[[Category: Lieberman, R L]]

OCA at 12:14, 6 November 2017

OCA — Mon, 06 Nov 2017 12:14:41 GMT

←Older revision		Revision as of 12:14, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='4x0k' size='340' side='right' caption='[[4x0k]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='4x0k' size='340' side='right' caption='[[4x0k]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x0k]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X0K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x0k]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X0K FirstGlance]. <br>
	</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=4x0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0k OCA], [http://pdbe.org/4x0k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x0k RCSB], [http://www.ebi.ac.uk/pdbsum/4x0k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0k ProSAT]</span></td></tr>		</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=4x0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0k OCA], [http://pdbe.org/4x0k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x0k RCSB], [http://www.ebi.ac.uk/pdbsum/4x0k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0k ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Johnson, J L]]		[[Category: Johnson, J L]]
	[[Category: Lieberman, R L]]		[[Category: Lieberman, R L]]

OCA at 18:40, 1 February 2017

OCA — Wed, 01 Feb 2017 18:40:26 GMT

←Older revision		Revision as of 18:40, 1 February 2017
Line 1:		Line 1:
		+
	==Engineered Fab fragment specific for EYMPME (EE) peptide==		==Engineered Fab fragment specific for EYMPME (EE) peptide==
	<StructureSection load='4x0k' size='340' side='right' caption='[[4x0k]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='4x0k' size='340' side='right' caption='[[4x0k]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x0k]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X0K FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x0k]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X0K FirstGlance]. <br>
-	</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=4x0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x0k RCSB], [http://www.ebi.ac.uk/pdbsum/4x0k PDBsum]</span></td></tr>	+	</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=4x0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0k OCA], [http://pdbe.org/4x0k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x0k RCSB], [http://www.ebi.ac.uk/pdbsum/4x0k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 13:		Line 14:
	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 4x0k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:43, 22 April 2015

OCA — Wed, 22 Apr 2015 06:43:53 GMT

←Older revision		Revision as of 06:43, 22 April 2015
Line 5:		Line 5:
	</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=4x0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x0k RCSB], [http://www.ebi.ac.uk/pdbsum/4x0k PDBsum]</span></td></tr>		</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=4x0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x0k RCSB], [http://www.ebi.ac.uk/pdbsum/4x0k PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Crystallization chaperones are attracting increasing interest as a route to crystal growth and structure elucidation of difficult targets such as membrane proteins. While strategies to date have typically employed protein-specific chaperones, a peptide-specific chaperone to crystallize multiple cognate peptide epitope-containing client proteins is envisioned. This would eliminate the target-specific chaperone-production step and streamline the co-crystallization process. Previously, protein engineering and directed evolution were used to generate a single-chain variable (scFv) antibody fragment with affinity for the peptide sequence EYMPME (scFv/EE). This report details the conversion of scFv/EE to an anti-EE Fab format (Fab/EE) followed by its biophysical characterization. The addition of constant chains increased the overall stability and had a negligible impact on the antigen affinity. The 2.0 A resolution crystal structure of Fab/EE reveals contacts with larger surface areas than those of scFv/EE. Surface plasmon resonance, an enzyme-linked immunosorbent assay, and size-exclusion chromatography were used to assess Fab/EE binding to EE-tagged soluble and membrane test proteins: namely, the beta-barrel outer membrane protein intimin and alpha-helical A2a G protein-coupled receptor (A2aR). Molecular-dynamics simulation of the intimin constructs with and without Fab/EE provides insight into the energetic complexities of the co-crystallization approach.
		+
		+	Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization.,Johnson JL, Entzminger KC, Hyun J, Kalyoncu S, Heaner DP Jr, Morales IA, Sheppard A, Gumbart JC, Maynard JA, Lieberman RL Acta Crystallogr D Biol Crystallogr. 2015 Apr;71(Pt 4):896-906. doi:, 10.1107/S1399004715001856. Epub 2015 Mar 27. PMID:25849400<ref>PMID:25849400</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:18, 8 April 2015

OCA — Wed, 08 Apr 2015 11:18:08 GMT

←Older revision		Revision as of 11:18, 8 April 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Engineered Fab fragment specific for EYMPME (EE) peptide==
-		+	<StructureSection load='4x0k' size='340' side='right' caption='[[4x0k]], [[Resolution\|resolution]] 2.04Å' scene=''>
-	~~The entry~~ 4x0k is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4x0k]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X0K FirstGlance]. <br>
-	~~Authors~~: Johnson, J.L., Lieberman, R.L.	+	</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=4x0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x0k RCSB], [http://www.ebi.ac.uk/pdbsum/4x0k PDBsum]</span></td></tr>
-		+	</table>
-	~~Description~~: ~~Engineered Fab~~ fragment ~~specific for EYMPME (EE) peptide~~	+	__TOC__
-	[[Category: ~~Unreleased Structures~~]]	+	</StructureSection>
-	[[Category: ~~Johnson, J.L~~]]	+	[[Category: Johnson, J L]]
-	[[Category: ~~Lieberman, R.L~~]]	+	[[Category: Lieberman, R L]]
		+	[[Category: Antibody fragment]]
		+	[[Category: Crystallization chaperone]]
		+	[[Category: Fab fragment]]
		+	[[Category: Immune system]]

OCA at 09:08, 4 March 2015

OCA — Wed, 04 Mar 2015 09:08:59 GMT

←Older revision		Revision as of 09:08, 4 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4x0k is ON HOLD	+	The entry 4x0k is ON HOLD until Paper Publication

	Authors: Johnson, J.L., Lieberman, R.L.		Authors: Johnson, J.L., Lieberman, R.L.

OCA at 20:18, 24 December 2014

OCA — Wed, 24 Dec 2014 20:18:06 GMT

←Older revision		Revision as of 20:18, 24 December 2014
Line 6:		Line 6:

	Description: Engineered Fab fragment specific for EYMPME (EE) peptide		Description: Engineered Fab fragment specific for EYMPME (EE) peptide
		+	[[Category: Unreleased Structures]]
		+	[[Category: Johnson, J.L]]
		+	[[Category: Lieberman, R.L]]

OCA: Protected "4x0k" [edit=sysop:move=sysop]

OCA — Wed, 03 Dec 2014 08:44:07 GMT

Protected "4x0k" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:44, 3 December 2014