6tk6

From Proteopedia

(Difference between revisions)

Revision as of 13:03, 24 January 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 20ms

Structural highlights

6tk6 is a 1 chain structure with sequence from Dokdonia eikasta. 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

Function

N0DKS8_9FLAO

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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. Femtosecond-to-millisecond structural changes in a light-driven sodium pump. Nature. 2020 May 20. pii: 10.1038/s41586-020-2307-8. doi:, 10.1038/s41586-020-2307-8. PMID:32499654 doi:http://dx.doi.org/10.1038/s41586-020-2307-8

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6tk6"

@@ Line 3: / Line 3: @@
 <StructureSection load='6tk6' size='340' side='right'caption='[[6tk6]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6tk6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cip_108743 Cip 108743]. 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 [http://proteopedia.org/fgij/fg.htm?mol=6TK6 FirstGlance]. <br>
+<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>
-</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>
+</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NaR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=308116 CIP 108743])</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'>[http://proteopedia.org/fgij/fg.htm?mol=6tk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tk6 OCA], [http://pdbe.org/6tk6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tk6 RCSB], [http://www.ebi.ac.uk/pdbsum/6tk6 PDBsum], [http://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>
+== Function ==
+[https://www.uniprot.org/uniprot/N0DKS8_9FLAO N0DKS8_9FLAO]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 19: @@
 </div>
 <div class="pdbe-citations 6tk6" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Rhodopsin 3D structures|Rhodopsin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Cip 108743]]
+[[Category: Dokdonia eikasta]]
 [[Category: Large Structures]]
-[[Category: Benoit, R]]
+[[Category: Benoit R]]
-[[Category: Bruenle, S]]
+[[Category: Bruenle S]]
-[[Category: Cirelli, C]]
+[[Category: Cirelli C]]
-[[Category: Deupi, X]]
+[[Category: Deupi X]]
-[[Category: Dworkowski, F]]
+[[Category: Dworkowski F]]
-[[Category: Ehrenberg, D]]
+[[Category: Ehrenberg D]]
-[[Category: Furrer, A]]
+[[Category: Furrer A]]
-[[Category: Gashi, D]]
+[[Category: Gashi D]]
-[[Category: Gruhl, T]]
+[[Category: Gruhl T]]
-[[Category: Heberle, J]]
+[[Category: Heberle J]]
-[[Category: James, D]]
+[[Category: James D]]
-[[Category: Johnson, P]]
+[[Category: Johnson P]]
-[[Category: Kar, R]]
+[[Category: Kar R]]
-[[Category: Kekilli, D]]
+[[Category: Kekilli D]]
-[[Category: Knopp, G]]
+[[Category: Knopp G]]
-[[Category: Martiel, I]]
+[[Category: Martiel I]]
-[[Category: Milne, C]]
+[[Category: Milne C]]
-[[Category: Mous, S]]
+[[Category: Mous S]]
-[[Category: Nass, K]]
+[[Category: Nass K]]
-[[Category: Nogly, P]]
+[[Category: Nogly P]]
-[[Category: Ozerov, D]]
+[[Category: Ozerov D]]
-[[Category: Panneels, V]]
+[[Category: Panneels V]]
-[[Category: Schapiro, I]]
+[[Category: Schapiro I]]
-[[Category: Schertler, G F.X]]
+[[Category: Schertler GFX]]
-[[Category: Skopintsev, P]]
+[[Category: Skopintsev P]]
-[[Category: Standfuss, J]]
+[[Category: Standfuss J]]
-[[Category: Weinert, T]]
+[[Category: Weinert T]]
-[[Category: Wranik, M]]
+[[Category: Wranik M]]
-[[Category: Membrane protein]]
-[[Category: Room-temperature]]
-[[Category: Serial femtosecond crystallograpy]]
-[[Category: Sodium pumping rhodopsin]]
-[[Category: Time-resolved]]

6tk6

From Proteopedia

Revision as of 13:03, 24 January 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 20ms

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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