This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1r84

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:10, 17 April 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1r84.jpg|left|200px]]
 
-
{{Structure
+
==NMR structure of the 13-cis-15-syn retinal in dark_adapted bacteriorhodopsin==
-
|PDB= 1r84 |SIZE=350|CAPTION= <scene name='initialview01'>1r84</scene>
+
<StructureSection load='1r84' size='340' side='right'caption='[[1r84]]' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=RET:RETINAL'>RET</scene>
+
<table><tr><td colspan='2'>[[1r84]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R84 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R84 FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-
|GENE=
+
<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=1r84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r84 OCA], [https://pdbe.org/1r84 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r84 RCSB], [https://www.ebi.ac.uk/pdbsum/1r84 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r84 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/r8/1r84_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=1r84 ConSurf].
 +
<div style="clear:both"></div>
-
'''NMR structure of the 13-cis-15-syn retinal in dark_adapted bacteriorhodopsin'''
+
==See Also==
-
 
+
*[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
The two forms of bacteriorhodopsin present in the dark-adapted state, containing either all-trans or 13-cis,15-syn retinal, were examined by using solution state NMR, and their structures were determined. Comparison of the all-trans and the 13-cis,15-syn forms shows a shift in position of about 0.25 A within the pocket of the protein. Comparing this to the 13-cis,15-anti chromophore of the catalytic cycle M-intermediate structure, the 13-cis,15-syn form demonstrates a less pronounced up-tilt of the retinal C12[bond]C14 region, while leaving W182 and T178 essentially unchanged. The N[bond]H dipole of the Schiff base orients toward the extracellular side in both forms, however, it reorients toward the intracellular side in the 13-cis,15-anti configuration to form the catalytic M-intermediate. Thus, the change of the N[bond]H dipole is considered primarily responsible for energy storage, conformation changes of the protein, and the deprotonation of the Schiff base. The structural similarity of the all-trans and 13-cis,15-syn forms is taken as strong evidence for the ion dipole dragging model by which proton (hydroxide ion) translocation follows the change of the dipole.
+
-
 
+
-
==About this Structure==
+
-
1R84 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=1R84 OCA].
+
-
 
+
-
==Reference==
+
-
The structures of the active center in dark-adapted bacteriorhodopsin by solution-state NMR spectroscopy., Patzelt H, Simon B, terLaak A, Kessler B, Kuhne R, Schmieder P, Oesterhelt D, Oschkinat H, Proc Natl Acad Sci U S A. 2002 Jul 23;99(15):9765-70. Epub 2002 Jul 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12119389 12119389]
+
[[Category: Halobacterium salinarum]]
[[Category: Halobacterium salinarum]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Kessler, B.]]
+
[[Category: Kessler B]]
-
[[Category: Kuhne, R.]]
+
[[Category: Kuhne R]]
-
[[Category: Laak, A Ter.]]
+
[[Category: Oesterhaelt D]]
-
[[Category: Oesterhaelt, D.]]
+
[[Category: Oschkinat H]]
-
[[Category: Oschkinat, H.]]
+
[[Category: Patzelt H]]
-
[[Category: Patzelt, H.]]
+
[[Category: Schmieder P]]
-
[[Category: Schmieder, P.]]
+
[[Category: Simon B]]
-
[[Category: Simon, B.]]
+
[[Category: Ter Laak A]]
-
[[Category: RET]]
+
-
[[Category: haloarchea]]
+
-
[[Category: membrane protein]]
+
-
[[Category: nmr]]
+
-
[[Category: photoreceptor]]
+
-
[[Category: proton pump]]
+
-
[[Category: proton transport]]
+
-
[[Category: retinal protein]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:48:07 2008''
+

Current revision

NMR structure of the 13-cis-15-syn retinal in dark_adapted bacteriorhodopsin

PDB ID 1r84

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1r84"
Personal tools