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| | <StructureSection load='3a7k' size='340' side='right'caption='[[3a7k]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='3a7k' size='340' side='right'caption='[[3a7k]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3a7k]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Natronomonas_pharaonis_dsm_2160 Natronomonas pharaonis dsm 2160]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A7K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3A7K FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3a7k]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Natronomonas_pharaonis_DSM_2160 Natronomonas pharaonis DSM 2160]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A7K FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=22B:BACTERIORUBERIN'>22B</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</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]] 2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3a4b|3a4b]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=22B:BACTERIORUBERIN'>22B</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</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=3a7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a7k OCA], [http://pdbe.org/3a7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3a7k RCSB], [http://www.ebi.ac.uk/pdbsum/3a7k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3a7k 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=3a7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a7k OCA], [https://pdbe.org/3a7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a7k RCSB], [https://www.ebi.ac.uk/pdbsum/3a7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a7k ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Natronomonas pharaonis dsm 2160]] | + | [[Category: Natronomonas pharaonis DSM 2160]] |
| - | [[Category: Kouyama, T]] | + | [[Category: Kouyama T]] |
| - | [[Category: Light-driven chloride ion pump]]
| + | |
| - | [[Category: Membrane protein]]
| + | |
| - | [[Category: Retinal protein]]
| + | |
| - | [[Category: Trimeric bacterioruberin-protein complex]]
| + | |
| Structural highlights
3a7k is a 3 chain structure with sequence from Natronomonas pharaonis DSM 2160. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The light-driven chloride pump halorhodopsin from Natronomonas pharaonis (phR) crystallised into the monoclinic space group C2, with a phR trimer per the asymmetric unit. Diffraction data at 2.0-A resolution showed that the carotenoid bacterioruberin binds to crevices between adjacent protein subunits in the trimeric assembly. Besides seven transmembrane helices (A to G) that characterise archaeal rhodopsins, the phR protomer possesses an amphipathic alpha-helix (A') at the N-terminus. This helix, together with a long loop between helices B and C, forms a hydrophobic cap that covers the extracellular surface and prevents a rapid ion exchange between the active centre and the extracellular medium. The retinal bound to Lys256 in helix G takes on an all-trans configuration with the Schiff base being hydrogen-bonded to a water molecule. The Schiff base also interacts with Asp252 and a chloride ion, the latter being fixed by two polar groups (Thr126 and Ser130) in helix C. In the anion uptake pathway, four ionisable residues (Arg123, Glu234, Arg176 and His100) and seven water molecules are aligned to form a long hydrogen-bonding network. Conversely, the cytoplasmic half is filled mostly by hydrophobic residues, forming a large energetic barrier against the transport of anion. The height of this barrier would be lowered substantially if the cytoplasmic half functions as a proton/HCl antiporter. Interestingly, there is a long cavity extending from the main-chain carbonyl of Lys256 to Thr71 in helix B. This cavity, which is commonly seen in halobacterial light-driven proton pumps, is one possible pathway that is utilised for a water-mediated proton transfer from the cytoplasmic medium to the anion, which is relocated to the cytoplasmic channel during the photocycle.
Crystal structure of the light-driven chloride pump halorhodopsin from Natronomonas pharaonis.,Kouyama T, Kanada S, Takeguchi Y, Narusawa A, Murakami M, Ihara K J Mol Biol. 2010 Feb 26;396(3):564-79. Epub 2009 Dec 1. PMID:19961859[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kouyama T, Kanada S, Takeguchi Y, Narusawa A, Murakami M, Ihara K. Crystal structure of the light-driven chloride pump halorhodopsin from Natronomonas pharaonis. J Mol Biol. 2010 Feb 26;396(3):564-79. Epub 2009 Dec 1. PMID:19961859 doi:10.1016/j.jmb.2009.11.061
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