View source for 6vbg


==Lactose permease complex with thiodigalactoside and nanobody 9043==
<StructureSection load='6vbg' size='340' side='right'caption='[[6vbg]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6vbg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VBG FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=YIO:(2R,3R,4S,5R,6S)-2-(HYDROXYMETHYL)-6-SULFANYL-OXANE-3,4,5-TRIOL'>YIO</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=6vbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vbg OCA], [https://pdbe.org/6vbg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vbg RCSB], [https://www.ebi.ac.uk/pdbsum/6vbg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vbg ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The structure of lactose permease, stabilized in a periplasmic open conformation by two Gly to Trp replacements (LacYww) and complexed with a nanobody directed against this conformation, provides the highest resolution structure of the symporter. The nanobody binds in a different manner than two other nanobodies made against the same mutant, which also bind to the same general region on the periplasmic side. This region of the protein may represent an immune hotspot. The CDR3 loop of the nanobody is held by hydrogen bonds in a conformation that partially blocks access to the substrate-binding site. As a result, kon and koff for galactoside binding to either LacY or the double mutant complexed with the nanobody are lower than for the other two LacY/nanobody complexes though the Kd values are similar, reflecting the fact that the nanobodies rigidify structures along the pathway. While the wild-type LacY/nanobody complex clearly stabilizes a similar 'extracellular open' conformation in solution, judged by binding kinetics, the complex with wild-type LacY did not yet crystallize, suggesting the nanobody does not bind strongly enough to shift the equilibrium to stabilize a periplasmic side-open conformation suitable for crystallization. However, the similarity of the galactoside binding kinetics for the nanobody-bound complexes with wild type LacY and with LacYWW indicates that they have similar structures, showing that the reported co-structures reliably show nanobody interactions with LacY.

Diversity in kinetics correlated with structure in nano body-stabilized LacY.,Kumar H, Finer-Moore J, Smirnova I, Kasho V, Pardon E, Steyaert J, Kaback HR, Stroud RM PLoS One. 2020 May 7;15(5):e0232846. doi: 10.1371/journal.pone.0232846. , eCollection 2020. PMID:32380514<ref>PMID:32380514</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6vbg" style="background-color:#fffaf0;"></div>

==See Also==
*[[Lactose Permease|Lactose Permease]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Lama glama]]
[[Category: Large Structures]]
[[Category: Finer-Moore J]]
[[Category: Kaback HR]]
[[Category: Kasho V]]
[[Category: Kumar H]]
[[Category: Pardon E]]
[[Category: Smirnova I]]
[[Category: Steyart J]]
[[Category: Stroud RM]]