1dv6: Difference between revisions

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-[[Image:1dv6.gif|left|200px]]<br /><applet load="1dv6" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1dv6, resolution 2.50&Aring;" />
-'''PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE WITH THE PROTON TRANSFER INHIBITOR ZN2+'''<br />
-==Overview==
+==PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE WITH THE PROTON TRANSFER INHIBITOR ZN2+==
-The reaction center (RC) from Rhodobacter sphaeroides couples light-driven electron transfer to protonation of a bound quinone acceptor molecule, Q(B), within the RC. The binding of Cd(2+) or Zn(2+) has been previously shown to inhibit the rate of reduction and protonation of Q(B). We report here on the metal binding site, determined by x-ray diffraction at 2.5-A resolution, obtained from RC crystals that were soaked in the presence of the metal. The structures were refined to R factors of 23% and 24% for the Cd(2+) and Zn(2+) complexes, respectively. Both metals bind to the same location, coordinating to Asp-H124, His-H126, and His-H128. The rate of electron transfer from Q(A)(-) to Q(B) was measured in the Cd(2+)-soaked crystal and found to be the same as in solution in the presence of Cd(2+). In addition to the changes in the kinetics, a structural effect of Cd(2+) on Glu-H173 was observed. This residue was well resolved in the x-ray structure-i.e., ordered-with Cd(2+) bound to the RC, in contrast to its disordered state in the absence of Cd(2+), which suggests that the mobility of Glu-H173 plays an important role in the rate of reduction of Q(B). The position of the Cd(2+) and Zn(2+) localizes the proton entry into the RC near Asp-H124, His-H126, and His-H128. Based on the location of the metal, likely pathways of proton transfer from the aqueous surface to Q(B) are proposed.
+<StructureSection load='1dv6' size='340' side='right'caption='[[1dv6]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1dv6]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides Cereibacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DV6 FirstGlance]. <br>
-DV6 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides] with <scene name='pdbligand=FE2:'>FE2</scene>, <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=BCL:'>BCL</scene>, <scene name='pdbligand=BPH:'>BPH</scene>, <scene name='pdbligand=U10:'>U10</scene> and <scene name='pdbligand=LDA:'>LDA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV6 OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv6 OCA], [https://pdbe.org/1dv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dv6 RCSB], [https://www.ebi.ac.uk/pdbsum/1dv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv6 ProSAT]</span></td></tr>
-Determination of the binding sites of the proton transfer inhibitors Cd2+ and Zn2+ in bacterial reaction centers., Axelrod HL, Abresch EC, Paddock ML, Okamura MY, Feher G, Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1542-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10677497 10677497]
+</table>
-[[Category: Protein complex]]
+== Function ==
-[[Category: Rhodobacter sphaeroides]]
+[https://www.uniprot.org/uniprot/RCEL_CERSP RCEL_CERSP] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.
-[[Category: Abresch, E C.]]
+== Evolutionary Conservation ==
-[[Category: Axelrod, H L.]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Feher, G.]]
+Check<jmol>
-[[Category: Okamura, M Y.]]
+  <jmolCheckbox>
-[[Category: Paddock, M L.]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/1dv6_consurf.spt"</scriptWhenChecked>
-[[Category: BCL]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: BPH]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: CL]]
+  </jmolCheckbox>
-[[Category: FE2]]
+</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=1dv6 ConSurf].
-[[Category: LDA]]
+<div style="clear:both"></div>
-[[Category: U10]]
+__TOC__
-[[Category: ZN]]
+</StructureSection>
-[[Category: bacterial photosynthesis]]
+[[Category: Cereibacter sphaeroides]]
-[[Category: cation binding]]
+[[Category: Large Structures]]
-[[Category: integral membrane protein]]
+[[Category: Abresch EC]]
-[[Category: metal ion binding]]
+[[Category: Axelrod HL]]
-[[Category: proton transfer]]
+[[Category: Feher G]]
-[[Category: rhodobacter sphaeroides]]
+[[Category: Okamura MY]]
-[[Category: x-ray crystallography]]
+[[Category: Paddock ML]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:20:46 2008''