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1vjm
From Proteopedia
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| - | [[Image:1vjm.gif|left|200px]]<br /><applet load="1vjm" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="1vjm, resolution 2.3Å" /> | ||
| - | '''Deformation of helix C in the low-temperature L-intermediate of bacteriorhodopsin'''<br /> | ||
| - | == | + | ==Deformation of helix C in the low-temperature L-intermediate of bacteriorhodopsin== |
| + | <StructureSection load='1vjm' size='340' side='right'caption='[[1vjm]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[1vjm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_sp. Halobacterium sp.]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1r3p 1r3p]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VJM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VJM 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]] 2.3Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=1vjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vjm OCA], [https://pdbe.org/1vjm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vjm RCSB], [https://www.ebi.ac.uk/pdbsum/1vjm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vjm ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA] Light-driven proton pump. | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vj/1vjm_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vjm ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
X-ray and electron diffraction studies of specific reaction intermediates, or reaction intermediate analogues, have produced a consistent picture of the structural mechanism of light-driven proton pumping by bacteriorhodopsin. Of central importance within this picture is the structure of the L-intermediate, which follows the retinal all-trans to 13-cis photoisomerization step of the K-intermediate and sets the stage for the primary proton transfer event from the positively charged Schiff base to the negatively charged Asp-85. Here we report the structural changes in bacteriorhodopsin following red light illumination at 150 K. Single crystal microspectrophotometry showed that only the L-intermediate is populated in three-dimensional crystals under these conditions. The experimental difference Fourier electron density map and refined crystallographic structure were consistent with those previously presented (Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2000) Nature 406, 645-648; Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2001) Photochem. Photobiol. 74, 794-804). Based on the refined crystallographic structures, molecular dynamic simulations were used to examine the influence of the conformational change of the protein that is associated with the K-to-L transition on retinal dynamics. Implications regarding the structural mechanism for proton pumping by bacteriorhodopsin are discussed. | X-ray and electron diffraction studies of specific reaction intermediates, or reaction intermediate analogues, have produced a consistent picture of the structural mechanism of light-driven proton pumping by bacteriorhodopsin. Of central importance within this picture is the structure of the L-intermediate, which follows the retinal all-trans to 13-cis photoisomerization step of the K-intermediate and sets the stage for the primary proton transfer event from the positively charged Schiff base to the negatively charged Asp-85. Here we report the structural changes in bacteriorhodopsin following red light illumination at 150 K. Single crystal microspectrophotometry showed that only the L-intermediate is populated in three-dimensional crystals under these conditions. The experimental difference Fourier electron density map and refined crystallographic structure were consistent with those previously presented (Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2000) Nature 406, 645-648; Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2001) Photochem. Photobiol. 74, 794-804). Based on the refined crystallographic structures, molecular dynamic simulations were used to examine the influence of the conformational change of the protein that is associated with the K-to-L transition on retinal dynamics. Implications regarding the structural mechanism for proton pumping by bacteriorhodopsin are discussed. | ||
| - | + | Deformation of helix C in the low temperature L-intermediate of bacteriorhodopsin.,Edman K, Royant A, Larsson G, Jacobson F, Taylor T, van der Spoel D, Landau EM, Pebay-Peyroula E, Neutze R J Biol Chem. 2004 Jan 16;279(3):2147-58. Epub 2003 Oct 7. PMID:14532280<ref>PMID:14532280</ref> | |
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| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 1vjm" style="background-color:#fffaf0;"></div> | |
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| - | + | ==See Also== | |
| + | *[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Halobacterium sp]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Edman K]] | ||
| + | [[Category: Jacobson F]] | ||
| + | [[Category: Landau EM]] | ||
| + | [[Category: Larsson G]] | ||
| + | [[Category: Neutze R]] | ||
| + | [[Category: Pebay-Peyroula E]] | ||
| + | [[Category: Royant A]] | ||
| + | [[Category: Taylor T]] | ||
| + | [[Category: Van der Spoel D]] | ||
Current revision
Deformation of helix C in the low-temperature L-intermediate of bacteriorhodopsin
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