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| | ==Synchrotron structure of light-driven chloride pump having an NTQ motif== | | ==Synchrotron structure of light-driven chloride pump having an NTQ motif== |
| - | <StructureSection load='5ztk' size='340' side='right' caption='[[5ztk]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='5ztk' size='340' side='right'caption='[[5ztk]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5ztk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Flavobacteria_bacterium_s1-08 Flavobacteria bacterium s1-08]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZTK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZTK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5ztk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nonlabens_marinus_S1-08 Nonlabens marinus S1-08]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZTK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZTK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</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]] 1.75Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ClR, NMS_1267 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1454201 Flavobacteria bacterium S1-08])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ztk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ztk OCA], [http://pdbe.org/5ztk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ztk RCSB], [http://www.ebi.ac.uk/pdbsum/5ztk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ztk 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=5ztk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ztk OCA], [https://pdbe.org/5ztk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ztk RCSB], [https://www.ebi.ac.uk/pdbsum/5ztk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ztk ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/W8VZW3_9FLAO W8VZW3_9FLAO] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 5ztk" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5ztk" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Rhodopsin 3D structures|Rhodopsin 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Flavobacteria bacterium s1-08]] | + | [[Category: Large Structures]] |
| - | [[Category: Lee, W]] | + | [[Category: Nonlabens marinus S1-08]] |
| - | [[Category: Park, J H]] | + | [[Category: Lee W]] |
| - | [[Category: Park, S Y]] | + | [[Category: Park JH]] |
| - | [[Category: Yun, J H]] | + | [[Category: Park SY]] |
| - | [[Category: Chloride pump]] | + | [[Category: Yun JH]] |
| - | [[Category: Signaling protein]]
| + | |
| Structural highlights
Function
W8VZW3_9FLAO
Publication Abstract from PubMed
Non-cryogenic protein structures determined at ambient temperature may disclose significant information about protein activity. Chloride-pumping rhodopsin (ClR) exhibits a trend to hyperactivity induced by a change in the photoreaction rate due to a gradual decrease in temperature. Here, to track the structural changes that explain the differences in CIR activity resulting from these temperature changes, we used serial femtosecond X-ray crystallography (SFX) with an X-ray free electron laser (XFEL) to determine the non-cryogenic structure of ClR at a resolution of 1.85 A, and compared this structure with a cryogenic ClR structure obtained with synchrotron X-ray crystallography. The XFEL-derived ClR structure revealed that the all-trans retinal (ATR) region and positions of two coordinated chloride ions slightly differed from those of the synchrotron-derived structure. Moreover, the XFEL structure enabled identification of one additional water molecule forming a hydrogen bond network with a chloride ion. Analysis of the channel cavity and a difference distance matrix plot (DDMP) clearly revealed additional structural differences. B-factor information obtained from the non-cryogenic structure supported a motility change on the residual main- and sidechains as well as of chloride and water molecules due to temperature effects. Our results indicate that non-cryogenic structures and time-resolved XFEL experiments could contribute to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.
Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency.,Yun JH, Li X, Park JH, Wang Y, Ohki M, Jin Z, Lee W, Park SY, Hu H, Li C, Zatsepin N, Hunter MS, Sierra RG, Koralek J, Yoon CH, Cho HS, Weierstall U, Tang L, Liu H, Lee W J Biol Chem. 2018 Nov 19. pii: RA118.004038. doi: 10.1074/jbc.RA118.004038. PMID:30455349[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yun JH, Li X, Park JH, Wang Y, Ohki M, Jin Z, Lee W, Park SY, Hu H, Li C, Zatsepin N, Hunter MS, Sierra RG, Koralek J, Yoon CH, Cho HS, Weierstall U, Tang L, Liu H, Lee W. Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency. J Biol Chem. 2018 Nov 19. pii: RA118.004038. doi: 10.1074/jbc.RA118.004038. PMID:30455349 doi:http://dx.doi.org/10.1074/jbc.RA118.004038
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