6yc3: Difference between revisions
New page: '''Unreleased structure''' The entry 6yc3 is ON HOLD until Paper Publication Authors: Kovalev, K., Gushchin, I., Gordeliy, V. Description: Crystal structure of the light-driven sodium ... |
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==Crystal structure of the light-driven sodium pump KR2 in the pentameric form, pH 8.0== | |||
<StructureSection load='6yc3' size='340' side='right'caption='[[6yc3]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6yc3]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Dokdonia_eikasta Dokdonia eikasta]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6rew 6rew]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YC3 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]] 2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=RET:RETINAL'>RET</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=6yc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yc3 OCA], [https://pdbe.org/6yc3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yc3 RCSB], [https://www.ebi.ac.uk/pdbsum/6yc3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yc3 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/N0DKS8_9FLAO N0DKS8_9FLAO] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The light-driven sodium-pumping rhodopsin KR2 from Krokinobacter eikastus is the only non-proton cation active transporter with demonstrated potential for optogenetics. However, the existing structural data on KR2 correspond exclusively to its ground state, and show no sodium inside the protein, which hampers the understanding of sodium-pumping mechanism. Here we present crystal structure of the O-intermediate of the physiologically relevant pentameric form of KR2 at the resolution of 2.1 A, revealing a sodium ion near the retinal Schiff base, coordinated by N112 and D116 of the characteristic NDQ triad. We also obtained crystal structures of D116N and H30A variants, conducted metadynamics simulations and measured pumping activities of putative pathway mutants to demonstrate that sodium release likely proceeds alongside Q78 towards the structural sodium ion bound between KR2 protomers. Our findings highlight the importance of pentameric assembly for sodium pump function, and may be used for rational engineering of enhanced optogenetic tools. | |||
Molecular mechanism of light-driven sodium pumping.,Kovalev K, Astashkin R, Gushchin I, Orekhov P, Volkov D, Zinovev E, Marin E, Rulev M, Alekseev A, Royant A, Carpentier P, Vaganova S, Zabelskii D, Baeken C, Sergeev I, Balandin T, Bourenkov G, Carpena X, Boer R, Maliar N, Borshchevskiy V, Buldt G, Bamberg E, Gordeliy V Nat Commun. 2020 May 1;11(1):2137. doi: 10.1038/s41467-020-16032-y. PMID:32358514<ref>PMID:32358514</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Gordeliy | <div class="pdbe-citations 6yc3" style="background-color:#fffaf0;"></div> | ||
[[Category: Gushchin | |||
[[Category: Kovalev | ==See Also== | ||
*[[Rhodopsin 3D structures|Rhodopsin 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Dokdonia eikasta]] | |||
[[Category: Large Structures]] | |||
[[Category: Gordeliy V]] | |||
[[Category: Gushchin I]] | |||
[[Category: Kovalev K]] | |||
Latest revision as of 16:23, 24 January 2024
Crystal structure of the light-driven sodium pump KR2 in the pentameric form, pH 8.0Crystal structure of the light-driven sodium pump KR2 in the pentameric form, pH 8.0
Structural highlights
FunctionPublication Abstract from PubMedThe light-driven sodium-pumping rhodopsin KR2 from Krokinobacter eikastus is the only non-proton cation active transporter with demonstrated potential for optogenetics. However, the existing structural data on KR2 correspond exclusively to its ground state, and show no sodium inside the protein, which hampers the understanding of sodium-pumping mechanism. Here we present crystal structure of the O-intermediate of the physiologically relevant pentameric form of KR2 at the resolution of 2.1 A, revealing a sodium ion near the retinal Schiff base, coordinated by N112 and D116 of the characteristic NDQ triad. We also obtained crystal structures of D116N and H30A variants, conducted metadynamics simulations and measured pumping activities of putative pathway mutants to demonstrate that sodium release likely proceeds alongside Q78 towards the structural sodium ion bound between KR2 protomers. Our findings highlight the importance of pentameric assembly for sodium pump function, and may be used for rational engineering of enhanced optogenetic tools. Molecular mechanism of light-driven sodium pumping.,Kovalev K, Astashkin R, Gushchin I, Orekhov P, Volkov D, Zinovev E, Marin E, Rulev M, Alekseev A, Royant A, Carpentier P, Vaganova S, Zabelskii D, Baeken C, Sergeev I, Balandin T, Bourenkov G, Carpena X, Boer R, Maliar N, Borshchevskiy V, Buldt G, Bamberg E, Gordeliy V Nat Commun. 2020 May 1;11(1):2137. doi: 10.1038/s41467-020-16032-y. PMID:32358514[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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