2j8c: Difference between revisions

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-{{Seed}}
-[[Image:2j8c.png|left|200px]]
-<!--
+==X-ray high resolution structure of the photosynthetic reaction center from Rb. sphaeroides at pH 8 in the neutral state==
-The line below this paragraph, containing "STRUCTURE_2j8c", creates the "Structure Box" on the page.
+<StructureSection load='2j8c' size='340' side='right'caption='[[2j8c]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2j8c]] is a 3 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=2J8C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J8C FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.87&#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=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GGD:NONADEC-10-ENOIC+ACID+2-[3,4-DIHYDROXY-6-HYDROXYMETHYL-5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLOXY)-TETRAHYDRO-PYRAN-2-YLOXY]-1-OCTADEC-9-ENOYLOXYMETHYL-ETHYL+ESTER'>GGD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=PC1:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PC1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SPO:SPHEROIDENE'>SPO</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene></td></tr>
-{{STRUCTURE_2j8c|  PDB=2j8c  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2j8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j8c OCA], [https://pdbe.org/2j8c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j8c RCSB], [https://www.ebi.ac.uk/pdbsum/2j8c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j8c ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RCEH_CERSP RCEH_CERSP] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.
+== 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/j8/2j8c_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=2j8c ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of the photosynthetic reaction-center from Rhodobacter sphaeroides has been determined at four different pH values (6.5, 8.0, 9.0, 10.0) in the neutral and in charge separated states. At pH 8.0, in the neutral state, we obtain a resolution of 1.87 A, which is the best ever reported for the bacterial reaction center protein. Our crystallographic data confirm the existence of two different binding positions of the secondary quinone (QB). We observe a new orientation of QB in its distal position, which shows no ring-flip compared to the orientation in the proximal position. Datasets collected for the different pH values show a pH-dependence of the population of the proximal position. The new orientation of QB in the distal position and the pH-dependence could be confirmed by continuum electrostatics calculations. Our calculations are in agreement with the experimentally observed proton uptake upon charge separation. The high resolution of our crystallographic data allows us to identify new water molecules and external residues being involved in two previously described hydrogen bond proton channels. These extended proton-transfer pathways, ending at either of the two oxo-groups of QB in its proximal position, provide additional evidence that ring-flipping is not required for complete protonation of QB upon reduction.
-===X-RAY HIGH RESOLUTION STRUCTURE OF THE PHOTOSYNTHETIC REACTION CENTER FROM RB. SPHAEROIDES AT PH 8 IN THE NEUTRAL STATE===
+pH modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states.,Koepke J, Krammer EM, Klingen AR, Sebban P, Ullmann GM, Fritzsch G J Mol Biol. 2007 Aug 10;371(2):396-409. Epub 2007 May 10. PMID:17570397<ref>PMID:17570397</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17570397}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2j8c" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17570397 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17570397}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Cereibacter sphaeroides]]
-J8C is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J8C OCA].
+[[Category: Large Structures]]
+[[Category: Diehm R]]
-==Reference==
+[[Category: Fritzsch G]]
-pH modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states., Koepke J, Krammer EM, Klingen AR, Sebban P, Ullmann GM, Fritzsch G, J Mol Biol. 2007 Aug 10;371(2):396-409. Epub 2007 May 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17570397 17570397]
+[[Category: Koepke J]]
-[[Category: Protein complex]]
-[[Category: Rhodobacter sphaeroides]]
-[[Category: Diehm, R.]]
-[[Category: Fritzsch, G.]]
-[[Category: Koepke, J.]]
-[[Category: Bacteriochlorophyll]]
-[[Category: Binding positions of the secondary quinone qb]]
-[[Category: Cardiolipin]]
-[[Category: Chlorophyll]]
-[[Category: Chromophore]]
-[[Category: Electron transport]]
-[[Category: Glucosylgalactosyl diacylglycerol]]
-[[Category: Iron]]
-[[Category: Magnesium]]
-[[Category: Membrane]]
-[[Category: Metal-binding]]
-[[Category: Phosphatidylcholine]]
-[[Category: Photosynthesis]]
-[[Category: Proton translocation pathway]]
-[[Category: Reaction center]]
-[[Category: Transmembrane]]
-[[Category: Transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 09:00:00 2008''