5gry - Revision history

OCA at 11:40, 2 August 2023

OCA — Wed, 02 Aug 2023 11:40:36 GMT

←Older revision		Revision as of 11:40, 2 August 2023
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	<StructureSection load='5gry' size='340' side='right'caption='[[5gry]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='5gry' size='340' side='right'caption='[[5gry]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gry]] is a 2 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=5GRY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5GRY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gry]] is a 2 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=5GRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GRY FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5gru\|5gru]]~~, [[~~5grv~~\|~~5grv]], [[5grw\|5grw]], [[5grx\|5grx]], [[5grz\|5grz]], [[5gs0\|5gs0]], [[5gs1\|5gs1]], [[5gs2\|5gs2]], [[5gs3\|5gs3~~]]</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]] 1.639Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5gry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gry OCA], [~~http~~://pdbe.org/5gry PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gry RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gry PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gry 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=5gry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gry OCA], [https://pdbe.org/5gry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gry RCSB], [https://www.ebi.ac.uk/pdbsum/5gry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gry ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5gry" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5gry" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cho, G]]	+	[[Category: Cho G]]
-	[[Category: Kim~~, J H~~]]	+	[[Category: Kim JH]]
-	[[Category: Kim~~, J W~~]]	+	[[Category: Kim JW]]
-	[[Category: Lee, H]]	+	[[Category: Lee H]]
-	[[Category: Lee~~, J O~~]]	+	[[Category: Lee JO]]
-	[[Category: Song~~, D H~~]]	+	[[Category: Song DH]]
-	[[Category: Youn~~, S J]]~~	+	[[Category: Youn SJ]]
-	~~[[Category: Antibody fragment]]~~	+
-	~~[[Category: Diabody]]~~	+
-	~~[[Category: Disulfide bond]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 06:51, 13 May 2020

OCA — Wed, 13 May 2020 06:51:27 GMT

←Older revision		Revision as of 06:51, 13 May 2020
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	==Crystal structure of disulfide-bonded diabody==		==Crystal structure of disulfide-bonded diabody==
-	<StructureSection load='5gry' size='340' side='right' caption='[[5gry]], [[Resolution\|resolution]] 1.64Å' scene=''>	+	<StructureSection load='5gry' size='340' side='right'caption='[[5gry]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GRY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GRY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gry]] is a 2 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=5GRY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GRY FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gru\|5gru]], [[5grv\|5grv]], [[5grw\|5grw]], [[5grx\|5grx]], [[5grz\|5grz]], [[5gs0\|5gs0]], [[5gs1\|5gs1]], [[5gs2\|5gs2]], [[5gs3\|5gs3]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gru\|5gru]], [[5grv\|5grv]], [[5grw\|5grw]], [[5grx\|5grx]], [[5grz\|5grz]], [[5gs0\|5gs0]], [[5gs1\|5gs1]], [[5gs2\|5gs2]], [[5gs3\|5gs3]]</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=5gry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gry OCA], [http://pdbe.org/5gry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gry RCSB], [http://www.ebi.ac.uk/pdbsum/5gry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gry ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5gry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gry OCA], [http://pdbe.org/5gry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gry RCSB], [http://www.ebi.ac.uk/pdbsum/5gry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gry 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: Large Structures]]
	[[Category: Cho, G]]		[[Category: Cho, G]]
	[[Category: Kim, J H]]		[[Category: Kim, J H]]

OCA at 17:39, 19 October 2016

OCA — Wed, 19 Oct 2016 17:39:21 GMT

←Older revision		Revision as of 17:39, 19 October 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5gry is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of disulfide-bonded diabody==
		+	<StructureSection load='5gry' size='340' side='right' caption='[[5gry]], [[Resolution\|resolution]] 1.64Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5gry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GRY FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gru\|5gru]], [[5grv\|5grv]], [[5grw\|5grw]], [[5grx\|5grx]], [[5grz\|5grz]], [[5gs0\|5gs0]], [[5gs1\|5gs1]], [[5gs2\|5gs2]], [[5gs3\|5gs3]]</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=5gry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gry OCA], [http://pdbe.org/5gry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gry RCSB], [http://www.ebi.ac.uk/pdbsum/5gry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gry ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Building a sophisticated protein nano-assembly requires a method for linking protein components in a predictable and stable structure. Diabodies are engineered antibody fragments that are composed of two Fv domains connected by short peptide linkers. They are attractive candidates for mediators in assembling protein nano-structures because they can simultaneously bind to two different proteins and are rigid enough to be crystallized. However, comparison of previous crystal structures demonstrates that there is substantial structural diversity in the Fv interface region of diabodies and, therefore, reliable prediction of its structure is not trivial. Here, we present the crystal structures of ten mono- and bi-specific diabodies. We found that changing an arginine residue in the Fv interface to threonine greatly reduced the structural diversity of diabodies. We also found that one of the bispecific diabodies underwent an unexpected process of chain swapping yielding a non-functional monospecific diabody. In order to further reduce structural flexibility and prevent chain shuffling, we introduced disulfide bridges in the Fv interface regions. The disulfide-bridged diabodies have rigid and predictable structures and may have applications in crystallizing proteins, analyzing cryo-electron microscopic images and building protein nano-assemblies.

-	~~Authors:~~ Kim~~, J.H.~~, Song~~, D.H.~~, Youn~~, S.J.~~, Kim~~, J.W.~~, Cho, G., Lee, H., ~~Lee~~, J.O.	+	Crystal structures of mono- and bi-specific diabodies and reduction of their structural flexibility by introduction of disulfide bridges at the Fv interface.,Kim JH, Song DH, Youn SJ, Kim JW, Cho G, Kim SC, Lee H, Jin MS, Lee JO Sci Rep. 2016 Sep 29;6:34515. doi: 10.1038/srep34515. PMID:27682821<ref>PMID:27682821</ref>

-	~~Description: Crystal structure~~ of ~~disulfide-bonded diabody~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Kim, J.H]]~~	+	<div class="pdbe-citations 5gry" style="background-color:#fffaf0;"></div>
-	~~[[Category: Kim, J.W]]~~	+	== References ==
-	~~[[Category: Youn, S.J]]~~	+	<references/>
-	~~[[Category: Song, D.H]]~~	+	__TOC__
-	~~[[Category: Lee, J.O]]~~	+	</StructureSection>
-	~~[[Category: Lee, H]]~~	+
	[[Category: Cho, G]]		[[Category: Cho, G]]
		+	[[Category: Kim, J H]]
		+	[[Category: Kim, J W]]
		+	[[Category: Lee, H]]
		+	[[Category: Lee, J O]]
		+	[[Category: Song, D H]]
		+	[[Category: Youn, S J]]
		+	[[Category: Antibody fragment]]
		+	[[Category: Diabody]]
		+	[[Category: Disulfide bond]]
		+	[[Category: Immune system]]

OCA at 16:06, 5 October 2016

OCA — Wed, 05 Oct 2016 16:06:17 GMT

←Older revision		Revision as of 16:06, 5 October 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5gry is ON HOLD	+	The entry 5gry is ON HOLD until Paper Publication

	Authors: Kim, J.H., Song, D.H., Youn, S.J., Kim, J.W., Cho, G., Lee, H., Lee, J.O.		Authors: Kim, J.H., Song, D.H., Youn, S.J., Kim, J.W., Cho, G., Lee, H., Lee, J.O.

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

OCA — Fri, 09 Sep 2016 12:00:20 GMT

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

←Older revision

Revision as of 12:00, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5gry is ON HOLD Authors: Kim, J.H., Song, D.H., Youn, S.J., Kim, J.W., Cho, G., Lee, H., Lee, J.O. Description: Crystal structure of disulfide-bond...

OCA — Fri, 09 Sep 2016 12:00:18 GMT

New page: '''Unreleased structure''' The entry 5gry is ON HOLD Authors: Kim, J.H., Song, D.H., Youn, S.J., Kim, J.W., Cho, G., Lee, H., Lee, J.O. Description: Crystal structure of disulfide-bond...

New page

'''Unreleased structure'''

The entry 5gry is ON HOLD

Authors: Kim, J.H., Song, D.H., Youn, S.J., Kim, J.W., Cho, G., Lee, H., Lee, J.O.

Description: Crystal structure of disulfide-bonded diabody
[[Category: Unreleased Structures]]
[[Category: Kim, J.H]]
[[Category: Kim, J.W]]
[[Category: Youn, S.J]]
[[Category: Song, D.H]]
[[Category: Lee, J.O]]
[[Category: Lee, H]]
[[Category: Cho, G]]