1kg8: Difference between revisions

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-[[Image:1kg8.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1kg8", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1kg8|  PDB=1kg8  |  SCENE=  }}
-'''X-ray structure of an early-M intermediate of bacteriorhodopsin'''
+==X-ray structure of an early-M intermediate of bacteriorhodopsin==
+<StructureSection load='1kg8' size='340' side='right'caption='[[1kg8]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1kg8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KG8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KG8 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LI1:1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL'>LI1</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=1kg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kg8 OCA], [https://pdbe.org/1kg8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kg8 RCSB], [https://www.ebi.ac.uk/pdbsum/1kg8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kg8 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/kg/1kg8_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1kg8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of an early M-intermediate of the wild-type bacteriorhodopsin photocycle formed by actinic illumination at 230 K has been determined by x-ray crystallography to a resolution of 2.0 A. Three-dimensional crystals were trapped by illuminating with actinic light at 230 K, followed by quenching in liquid nitrogen. Amide I, amide II, and other infrared absorption bands, recorded from single bacteriorhodopsin crystals, confirm that the M-substate formed represents a structure that occurs early after deprotonation of the Schiff base. Rotation about the retinal C13-C14 double bond appears to be complete, but a relatively large torsion angle of 26 degrees is still seen for the C14-C15 bond. The intramolecular stress associated with the isomerization of retinal and the subsequent deprotonation of the Schiff base generates numerous small but experimentally measurable structural changes within the protein. Many of the residues that are displaced during the formation of the late M (M(N)) substate formed by three-dimensional crystals of the D96N mutant (Luecke et al., 1999b) are positioned, in early M, between their resting-state locations and the ones which they will adopt at the end of the M phase. The relatively small magnitude of atomic displacements observed in this intermediate, and the well-defined positions adopted by nearly all of the atoms in the structure, may make the formation of this structure favorable to model (simulate) by molecular dynamics.
-==Overview==
+Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle.,Facciotti MT, Rouhani S, Burkard FT, Betancourt FM, Downing KH, Rose RB, McDermott G, Glaeser RM Biophys J. 2001 Dec;81(6):3442-55. PMID:11721006<ref>PMID:11721006</ref>
-The structure of an early M-intermediate of the wild-type bacteriorhodopsin photocycle formed by actinic illumination at 230 K has been determined by x-ray crystallography to a resolution of 2.0 A. Three-dimensional crystals were trapped by illuminating with actinic light at 230 K, followed by quenching in liquid nitrogen. Amide I, amide II, and other infrared absorption bands, recorded from single bacteriorhodopsin crystals, confirm that the M-substate formed represents a structure that occurs early after deprotonation of the Schiff base. Rotation about the retinal C13-C14 double bond appears to be complete, but a relatively large torsion angle of 26 degrees is still seen for the C14-C15 bond. The intramolecular stress associated with the isomerization of retinal and the subsequent deprotonation of the Schiff base generates numerous small but experimentally measurable structural changes within the protein. Many of the residues that are displaced during the formation of the late M (M(N)) substate formed by three-dimensional crystals of the D96N mutant (Luecke et al., 1999b) are positioned, in early M, between their resting-state locations and the ones which they will adopt at the end of the M phase. The relatively small magnitude of atomic displacements observed in this intermediate, and the well-defined positions adopted by nearly all of the atoms in the structure, may make the formation of this structure favorable to model (simulate) by molecular dynamics.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-KG8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KG8 OCA].
+</div>
+<div class="pdbe-citations 1kg8" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle., Facciotti MT, Rouhani S, Burkard FT, Betancourt FM, Downing KH, Rose RB, McDermott G, Glaeser RM, Biophys J. 2001 Dec;81(6):3442-55. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11721006 11721006]
+*[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Halobacterium salinarum]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Betancourt, F M.]]
+[[Category: Betancourt FM]]
-[[Category: Burkard, F T.]]
+[[Category: Burkard FT]]
-[[Category: Downing, K H.]]
+[[Category: Downing KH]]
-[[Category: Facciotti, M T.]]
+[[Category: Facciotti MT]]
-[[Category: Glaeser, R M.]]
+[[Category: Glaeser RM]]
-[[Category: McDermott, G.]]
+[[Category: McDermott G]]
-[[Category: Rose, R B.]]
+[[Category: Rose RB]]
-[[Category: Rouhani, S.]]
+[[Category: Rouhani S]]
-[[Category: Bacteriorhodopsin]]
-[[Category: Intermediate]]
-[[Category: M-state]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 22:42:36 2008''