6tk6: Difference between revisions

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<StructureSection load='6tk6' size='340' side='right'caption='[[6tk6]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
<StructureSection load='6tk6' size='340' side='right'caption='[[6tk6]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6tk6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dokdonia_eikasta Dokdonia eikasta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TK6 FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TK6 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]] 1.6&#8491;</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]] 1.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LFA:EICOSANE'>LFA</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=6tk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tk6 OCA], [https://pdbe.org/6tk6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tk6 RCSB], [https://www.ebi.ac.uk/pdbsum/6tk6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tk6 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=6tk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tk6 OCA], [https://pdbe.org/6tk6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tk6 RCSB], [https://www.ebi.ac.uk/pdbsum/6tk6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tk6 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/N0DKS8_9FLAO N0DKS8_9FLAO]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Light-driven sodium pumps actively transport small cations across cellular membranes(1). These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience. Although the resting state structures of the prototypical sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) have been solved(2,3), it is unclear how structural alterations over time allow sodium to be translocated against a concentration gradient. Here, using the Swiss X-ray Free Electron Laser(4), we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds. Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds. Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond. In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit. These results provide direct molecular insight into the dynamics of active cation transport across biological membranes.
Femtosecond-to-millisecond structural changes in a light-driven sodium pump.,Skopintsev P, Ehrenberg D, Weinert T, James D, Kar RK, Johnson PJM, Ozerov D, Furrer A, Martiel I, Dworkowski F, Nass K, Knopp G, Cirelli C, Arrell C, Gashi D, Mous S, Wranik M, Gruhl T, Kekilli D, Brunle S, Deupi X, Schertler GFX, Benoit RM, Panneels V, Nogly P, Schapiro I, Milne C, Heberle J, Standfuss J Nature. 2020 May 20. pii: 10.1038/s41586-020-2307-8. doi:, 10.1038/s41586-020-2307-8. PMID:32499654<ref>PMID:32499654</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6tk6" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Rhodopsin 3D structures|Rhodopsin 3D structures]]
*[[Rhodopsin 3D structures|Rhodopsin 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Dokdonia eikasta]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Benoit R]]
[[Category: Benoit R]]

Latest revision as of 11:21, 17 October 2024

Femtosecond to millisecond structural changes in a light-driven sodium pump: Dark structure in neutral conditions with attached light datasets at 800fs, 2ps, 100ps, 1ns, 16ns, 1us, 30us, 150us, 1ms and 20msFemtosecond to millisecond structural changes in a light-driven sodium pump: Dark structure in neutral conditions with attached light datasets at 800fs, 2ps, 100ps, 1ns, 16ns, 1us, 30us, 150us, 1ms and 20ms

Structural highlights

Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

6tk6, resolution 1.60Å

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