6ir1: Difference between revisions
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<StructureSection load='6ir1' size='340' side='right'caption='[[6ir1]], [[Resolution|resolution]] 1.92Å' scene=''> | <StructureSection load='6ir1' size='340' side='right'caption='[[6ir1]], [[Resolution|resolution]] 1.92Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6ir1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[6ir1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anaplasma_marginale Anaplasma marginale] 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=6IR1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IR1 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.919Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CH6:{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CH6</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=6ir1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ir1 OCA], [https://pdbe.org/6ir1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ir1 RCSB], [https://www.ebi.ac.uk/pdbsum/6ir1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ir1 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=6ir1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ir1 OCA], [https://pdbe.org/6ir1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ir1 RCSB], [https://www.ebi.ac.uk/pdbsum/6ir1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ir1 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/X5DSL3_ANAMA X5DSL3_ANAMA] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Anaplasma | [[Category: Anaplasma marginale]] | ||
[[Category: | [[Category: Camelus bactrianus]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Chen | [[Category: Chen X]] | ||
[[Category: Ding | [[Category: Ding Y]] | ||
[[Category: Hu | [[Category: Hu RT]] | ||
[[Category: Wang | [[Category: Wang ZY]] | ||
Latest revision as of 13:26, 15 November 2023
Crystal structure of red fluorescent protein mCherry complexed with the nanobody LaM4 at 1.9 Angstron resolutionCrystal structure of red fluorescent protein mCherry complexed with the nanobody LaM4 at 1.9 Angstron resolution
Structural highlights
FunctionPublication Abstract from PubMedRed fluorescent proteins (RFPs) are powerful tools used in molecular biology research. Although RFP can be easily monitored in vivo, manipulation of RFP by suitable nanobodies binding to different epitopes of RFP is still desired. Thus, it is crucial to obtain structural information on how the different nanobodies interact with RFP. Here, we determined the crystal structures of the LaM2-mCherry and LaM4-mCherry complexes at 1.4 and 1.9 A resolution. Our results showed that LaM2 binds to the side of the mCherry beta-barrel, while LaM4 binds to the bottom of the beta-barrel. The distinct binding sites of LaM2 and LaM4 were further verified by isothermal titration calorimetry, fluorescence-based size exclusion chromatography, and dynamic light scattering assays. Mutation of the residues at the LaM2 or LaM4 binding interface to mCherry significantly decreased the binding affinity of the nanobody to mCherry. Our results also showed that LaM2 and LaM4 can bind to mCherry simultaneously, which is crucial for recruiting multiple operation elements to the RFP. The binding of LaM2 or LaM4 did not significantly change the chromophore environment of mCherry, which is important for fluorescence quantification assays, while several GFP nanobodies significantly altered the fluorescence. Our results provide atomic resolution interaction information on the binding of nanobodies LaM2 and LaM4 with mCherry, which is important for developing detection and manipulation methods for RFP-based biotechnology. Structural insights into the binding of nanobodies LaM2 and LaM4 to the red fluorescent protein mCherry.,Wang Z, Li L, Hu R, Zhong P, Zhang Y, Cheng S, Jiang H, Liu R, Ding Y Protein Sci. 2021 Nov;30(11):2298-2309. doi: 10.1002/pro.4194. Epub 2021 Oct 5. PMID:34562299[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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