7cd7 - Revision history

OCA at 09:22, 9 October 2024

2024-10-09T09:22:19Z

← Older revision		Revision as of 09:22, 9 October 2024
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7cd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cd7 OCA], [https://pdbe.org/7cd7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cd7 RCSB], [https://www.ebi.ac.uk/pdbsum/7cd7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cd7 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=7cd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cd7 OCA], [https://pdbe.org/7cd7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cd7 RCSB], [https://www.ebi.ac.uk/pdbsum/7cd7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cd7 ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Synthetic binding proteins that have the ability to bind with molecules can be generated using various protein domains as non-antibody scaffolds. These designer proteins have been used widely in research studies, as their properties overcome the disadvantages of using antibodies. Here, we describe the first application of a phage display to generate synthetic binding proteins using a sweet protein, monellin, as a non-antibody scaffold. Single-chain monellin (scMonellin), in which two polypeptide chains of natural monellin are connected by a short linker, has two loops on one side of the molecule. We constructed phage display libraries of scMonellin, in which the amino acid sequence of the two loops is diversified. To validate the performance of these libraries, we sorted them against the folding mutant of the green fluorescent protein variant (GFPuv) and yeast small ubiquitin-related modifier. We successfully obtained scMonellin variants exhibiting moderate but significant affinities for these target proteins. Crystal structures of one of the GFPuv-binding variants in complex with GFPuv revealed that the two diversified loops were involved in target recognition. scMonellin, therefore, represents a promising non-antibody scaffold in the design and generation of synthetic binding proteins. We termed the scMonellin-derived synthetic binding proteins 'SWEEPins'.

	A sweet protein monellin as a non-antibody scaffold for synthetic binding proteins.,Yasui N, Nakamura K, Yamashita A J Biochem. 2021 Jul 3;169(5):585-599. doi: 10.1093/jb/mvaa147. PMID:33386843<ref>PMID:33386843</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7cd7" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]		*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:05, 29 November 2023

2023-11-29T16:05:16Z

← Older revision		Revision as of 16:05, 29 November 2023
Line 1:		Line 1:

	====		==GFP-40/GFPuv complex, Form I==
	<StructureSection load='7cd7' size='340' side='right'caption='[[7cd7]]' scene=''>		<StructureSection load='7cd7' size='340' side='right'caption='[[7cd7]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>		<table><tr><td colspan='2'>[[7cd7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria] 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=7CD7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CD7 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=7cd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cd7 OCA], [https://pdbe.org/7cd7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cd7 RCSB], [https://www.ebi.ac.uk/pdbsum/7cd7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cd7 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]] 1.704Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene></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=7cd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cd7 OCA], [https://pdbe.org/7cd7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cd7 RCSB], [https://www.ebi.ac.uk/pdbsum/7cd7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cd7 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Synthetic binding proteins that have the ability to bind with molecules can be generated using various protein domains as non-antibody scaffolds. These designer proteins have been used widely in research studies, as their properties overcome the disadvantages of using antibodies. Here, we describe the first application of a phage display to generate synthetic binding proteins using a sweet protein, monellin, as a non-antibody scaffold. Single-chain monellin (scMonellin), in which two polypeptide chains of natural monellin are connected by a short linker, has two loops on one side of the molecule. We constructed phage display libraries of scMonellin, in which the amino acid sequence of the two loops is diversified. To validate the performance of these libraries, we sorted them against the folding mutant of the green fluorescent protein variant (GFPuv) and yeast small ubiquitin-related modifier. We successfully obtained scMonellin variants exhibiting moderate but significant affinities for these target proteins. Crystal structures of one of the GFPuv-binding variants in complex with GFPuv revealed that the two diversified loops were involved in target recognition. scMonellin, therefore, represents a promising non-antibody scaffold in the design and generation of synthetic binding proteins. We termed the scMonellin-derived synthetic binding proteins 'SWEEPins'.

			A sweet protein monellin as a non-antibody scaffold for synthetic binding proteins.,Yasui N, Nakamura K, Yamashita A J Biochem. 2021 Jul 3;169(5):585-599. doi: 10.1093/jb/mvaa147. PMID:33386843<ref>PMID:33386843</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7cd7" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Aequorea victoria]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Z-disk~~]]		[[Category: Synthetic construct]]
			[[Category: Yamashita A]]
			[[Category: Yasui N]]

OCA at 10:05, 14 July 2021

2021-07-14T10:05:23Z

← Older revision		Revision as of 10:05, 14 July 2021
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	<StructureSection load='7cd7' size='340' side='right'caption='[[7cd7]]' scene=''>		<StructureSection load='7cd7' size='340' side='right'caption='[[7cd7]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
	</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=7cd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cd7 OCA], [~~http~~://pdbe.org/7cd7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7cd7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7cd7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7cd7 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=7cd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cd7 OCA], [https://pdbe.org/7cd7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cd7 RCSB], [https://www.ebi.ac.uk/pdbsum/7cd7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cd7 ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 05:54, 20 January 2021

2021-01-20T05:54:32Z

← Older revision		Revision as of 05:54, 20 January 2021
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7cd7 ~~is ON HOLD until Paper Publication~~		====
			<StructureSection load='7cd7' size='340' side='right'caption='[[7cd7]]' scene=''>
	~~Authors~~: ~~Yasui, N~~.~~, Yamashita, A~~.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
	~~Description~~: ~~GFP~~-40/~~GFPuv complex~~, ~~Form I~~		</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=7cd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cd7 OCA], [http://pdbe.org/7cd7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7cd7 RCSB], [http://www.ebi.ac.uk/pdbsum/7cd7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7cd7 ProSAT]</span></td></tr>
	[[~~Category~~: ~~Unreleased Structures~~]]		</table>
	[[Category: ~~Yasui, N~~]]		__TOC__
	[[Category: ~~Yamashita, A~~]]		</StructureSection>
			[[Category: Large Structures]]
			[[Category: Z-disk]]

OCA at 11:25, 8 July 2020

2020-07-08T11:25:07Z

← Older revision		Revision as of 11:25, 8 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7cd7 is ON HOLD		The entry 7cd7 is ON HOLD until Paper Publication

	Authors: Yasui, N., Yamashita, A.		Authors: Yasui, N., Yamashita, A.

OCA: Protected "7cd7" [edit=sysop:move=sysop]

2020-06-24T18:56:17Z

Protected "7cd7" [edit=sysop:move=sysop]

← Older revision	Revision as of 18:56, 24 June 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7cd7 is ON HOLD Authors: Yasui, N., Yamashita, A. Description: GFP-40/GFPuv complex, Form I Category: Unreleased Structures [[Category: Yasui, ...

2020-06-24T18:56:16Z

New page: '''Unreleased structure''' The entry 7cd7 is ON HOLD Authors: Yasui, N., Yamashita, A. Description: GFP-40/GFPuv complex, Form I Category: Unreleased Structures [[Category: Yasui, ...

New page

'''Unreleased structure'''

The entry 7cd7 is ON HOLD

Authors: Yasui, N., Yamashita, A.

Description: GFP-40/GFPuv complex, Form I
[[Category: Unreleased Structures]]
[[Category: Yasui, N]]
[[Category: Yamashita, A]]