7e53 - Revision history

OCA at 16:46, 29 November 2023

OCA — Wed, 29 Nov 2023 16:46:34 GMT

←Older revision		Revision as of 16:46, 29 November 2023
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-	====	+	==Crystal structure of sfGFP complexed with the nanobody nb2 at 2.2 Angstron resolution==
-	<StructureSection load='7e53' size='340' side='right'caption='[[7e53]]' scene=''>	+	<StructureSection load='7e53' size='340' side='right'caption='[[7e53]], [[Resolution\|resolution]] 2.21Å' 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'>[[7e53]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria] and [https://en.wikipedia.org/wiki/Camelus_bactrianus Camelus bactrianus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E53 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E53 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=7e53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e53 OCA], [https://pdbe.org/7e53 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e53 RCSB], [https://www.ebi.ac.uk/pdbsum/7e53 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e53 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]] 2.21Å</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=7e53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e53 OCA], [https://pdbe.org/7e53 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e53 RCSB], [https://www.ebi.ac.uk/pdbsum/7e53 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e53 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A059PIQ0_AEQVI A0A059PIQ0_AEQVI]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Green fluorescent protein (GFP) and its derivatives are widely used in biomedical research, and the manipulation of GFP-tagged proteins by GFP-specific binders is highly desired. However, structural information on how these binders bind with GFP is still lacking. In this study, we determined the crystal structure of the nanobody Nb2 complexed with superfolder GFP (sfGFP) at a resolution of 2.2 A. Interestingly, although the complementarity-determining regions (CDRs) of Nb2 and LaG16 sequences were only 29.7% identical, they both bound to the same epitope of GFP and existed in the same orientation. Structural analysis indicated that they achieved similar binding characteristics through different mechanisms. We further verified the kinetics and thermodynamics of binding by biolayer interferometry (BLI) and isothermal titration calorimetry (ITC). Nb2 showed a slightly higher binding affinity for sfGFP than LaG16. The stability of GFP-specific nanobodies was verified by nano differential scanning fluorimetry (nanoDSF). Nb2 exhibited the highest melting temperature (Tm); thus, Nb2 is a promising GFP nanobody candidate for use in applications requiring harsh testing conditions. We also compared the binding sites of available GFP nanobodies and showed that some of them can simultaneously bind with GFP and assemble into multifunctional complexes to manipulate GFP-tagged target proteins. Our results provide atomic-scale binding information for Nb2-sfGFP, which is important for the further development of GFP-nanobody based fusion protein manipulation techniques.
		+
		+	Structural insights into two distinct nanobodies recognizing the same epitope of green fluorescent protein.,Zhong P, Wang Z, Cheng S, Zhang Y, Jiang H, Liu R, Ding Y Biochem Biophys Res Commun. 2021 Aug 6;565:57-63. doi: , 10.1016/j.bbrc.2021.05.089. Epub 2021 Jun 4. PMID:34098312<ref>PMID:34098312</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7e53" 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: Camelus bactrianus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Ding Y]]
		+	[[Category: Zhong PY]]

OCA at 11:40, 13 October 2021

OCA — Wed, 13 Oct 2021 11:40:42 GMT

←Older revision		Revision as of 11:40, 13 October 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7e53 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7e53' size='340' side='right'caption='[[7e53]]' scene=''>
-	~~Authors~~: ~~Ding, Y~~.~~, Zhong, P~~.Y.	+	== 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>
-	~~Description: Crystal structure of sfGFP complexed with~~ the ~~nanobody nb2 at 2~~.~~2 Angstron resolution~~	+	</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=7e53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e53 OCA], [https://pdbe.org/7e53 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e53 RCSB], [https://www.ebi.ac.uk/pdbsum/7e53 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e53 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Zhong~~, P.Y]]	+	__TOC__
-	[[Category: ~~Ding, Y~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 08:02, 12 May 2021

OCA — Wed, 12 May 2021 08:02:16 GMT

←Older revision		Revision as of 08:02, 12 May 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7e53 is ON HOLD	+	The entry 7e53 is ON HOLD until Paper Publication

	Authors: Ding, Y., Zhong, P.Y.		Authors: Ding, Y., Zhong, P.Y.

OCA: Protected "7e53" [edit=sysop:move=sysop]

OCA — Wed, 24 Feb 2021 05:34:39 GMT

Protected "7e53" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:34, 24 February 2021

OCA: New page: '''Unreleased structure''' The entry 7e53 is ON HOLD Authors: Ding, Y., Zhong, P.Y. Description: Crystal structure of sfGFP complexed with the nanobody nb2 at 2.2 Angstron resolution [...

OCA — Wed, 24 Feb 2021 05:34:38 GMT

New page: '''Unreleased structure''' The entry 7e53 is ON HOLD Authors: Ding, Y., Zhong, P.Y. Description: Crystal structure of sfGFP complexed with the nanobody nb2 at 2.2 Angstron resolution [...

New page

'''Unreleased structure'''

The entry 7e53 is ON HOLD

Authors: Ding, Y., Zhong, P.Y.

Description: Crystal structure of sfGFP complexed with the nanobody nb2 at 2.2 Angstron resolution
[[Category: Unreleased Structures]]
[[Category: Zhong, P.Y]]
[[Category: Ding, Y]]