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==Time-resolved serial femtosecond crystallography structure of light-driven chloride ion-pumping rhodopsin, NM-R3 : structure obtained 1 msec after photoexcitation with bromide ion== | ==Time-resolved serial femtosecond crystallography structure of light-driven chloride ion-pumping rhodopsin, NM-R3 : structure obtained 1 msec after photoexcitation with bromide ion== | ||
<StructureSection load='7vgu' size='340' side='right'caption='[[7vgu]]' scene=''> | <StructureSection load='7vgu' size='340' side='right'caption='[[7vgu]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VGU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VGU FirstGlance]. <br> | <table><tr><td colspan='2'>[[7vgu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VGU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VGU FirstGlance]. <br> | ||
</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=7vgu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vgu OCA], [https://pdbe.org/7vgu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vgu RCSB], [https://www.ebi.ac.uk/pdbsum/7vgu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vgu ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=HEX:HEXANE'>HEX</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=7vgu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vgu OCA], [https://pdbe.org/7vgu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vgu RCSB], [https://www.ebi.ac.uk/pdbsum/7vgu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vgu ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Light-driven chloride-pumping rhodopsins actively transport anions, including various halide ions, across cell membranes. Recent studies using time-resolved serial femtosecond crystallography (TR-SFX) have uncovered the structural changes and ion transfer mechanisms in light-driven cation-pumping rhodopsins. However, the mechanism by which the conformational changes pump an anion to achieve unidirectional ion transport, from the extracellular side to the cytoplasmic side, in anion-pumping rhodopsins remains enigmatic. We have collected TR-SFX data of Nonlabens marinus rhodopsin-3 (NM-R3), derived from a marine flavobacterium, at 10-micros and 1-ms time points after photoexcitation. Our structural analysis reveals the conformational alterations during ion transfer and after ion release. Movements of the retinal chromophore initially displace a conserved tryptophan to the cytoplasmic side of NM-R3, accompanied by a slight shift of the halide ion bound to the retinal. After ion release, the inward movements of helix C and helix G and the lateral displacements of the retinal block access to the extracellular side of NM-R3. Anomalous signal data have also been obtained from NM-R3 crystals containing iodide ions. The anomalous density maps provide insight into the halide binding site for ion transfer in NM-R3. | |||
Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers.,Hosaka T, Nomura T, Kubo M, Nakane T, Fangjia L, Sekine SI, Ito T, Murayama K, Ihara K, Ehara H, Kashiwagi K, Katsura K, Akasaka R, Hisano T, Tanaka T, Tanaka R, Arima T, Yamashita A, Sugahara M, Naitow H, Matsuura Y, Yoshizawa S, Tono K, Owada S, Nureki O, Kimura-Someya T, Iwata S, Nango E, Shirouzu M Proc Natl Acad Sci U S A. 2022 Mar 1;119(9). pii: 2117433119. doi:, 10.1073/pnas.2117433119. PMID:35197289<ref>PMID:35197289</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7vgu" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Rhodopsin 3D structures|Rhodopsin 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Hosaka T]] | [[Category: Hosaka, T]] | ||
[[Category: Kimura-Someya T]] | [[Category: Kimura-Someya, T]] | ||
[[Category: Luo F]] | [[Category: Luo, F]] | ||
[[Category: Nakane T]] | [[Category: Nakane, T]] | ||
[[Category: Nango E]] | [[Category: Nango, E]] | ||
[[Category: Shirouzu M]] | [[Category: Shirouzu, M]] | ||
[[Category: Membrane protein]] | |||
[[Category: Sacla serial femtosecond crystallography cell-free synthesis bacterial type rhodopsin chloride ion pump rhodopsin]] | |||
Revision as of 10:27, 9 March 2022
Time-resolved serial femtosecond crystallography structure of light-driven chloride ion-pumping rhodopsin, NM-R3 : structure obtained 1 msec after photoexcitation with bromide ionTime-resolved serial femtosecond crystallography structure of light-driven chloride ion-pumping rhodopsin, NM-R3 : structure obtained 1 msec after photoexcitation with bromide ion
Structural highlights
Publication Abstract from PubMedLight-driven chloride-pumping rhodopsins actively transport anions, including various halide ions, across cell membranes. Recent studies using time-resolved serial femtosecond crystallography (TR-SFX) have uncovered the structural changes and ion transfer mechanisms in light-driven cation-pumping rhodopsins. However, the mechanism by which the conformational changes pump an anion to achieve unidirectional ion transport, from the extracellular side to the cytoplasmic side, in anion-pumping rhodopsins remains enigmatic. We have collected TR-SFX data of Nonlabens marinus rhodopsin-3 (NM-R3), derived from a marine flavobacterium, at 10-micros and 1-ms time points after photoexcitation. Our structural analysis reveals the conformational alterations during ion transfer and after ion release. Movements of the retinal chromophore initially displace a conserved tryptophan to the cytoplasmic side of NM-R3, accompanied by a slight shift of the halide ion bound to the retinal. After ion release, the inward movements of helix C and helix G and the lateral displacements of the retinal block access to the extracellular side of NM-R3. Anomalous signal data have also been obtained from NM-R3 crystals containing iodide ions. The anomalous density maps provide insight into the halide binding site for ion transfer in NM-R3. Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers.,Hosaka T, Nomura T, Kubo M, Nakane T, Fangjia L, Sekine SI, Ito T, Murayama K, Ihara K, Ehara H, Kashiwagi K, Katsura K, Akasaka R, Hisano T, Tanaka T, Tanaka R, Arima T, Yamashita A, Sugahara M, Naitow H, Matsuura Y, Yoshizawa S, Tono K, Owada S, Nureki O, Kimura-Someya T, Iwata S, Nango E, Shirouzu M Proc Natl Acad Sci U S A. 2022 Mar 1;119(9). pii: 2117433119. doi:, 10.1073/pnas.2117433119. PMID:35197289[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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