1dv6: Difference between revisions

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New page: left|200px<br /><applet load="1dv6" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dv6, resolution 2.50Å" /> '''PHOTOSYNTHETIC REACT...
 
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[[Image:1dv6.gif|left|200px]]<br /><applet load="1dv6" size="450" 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>
1DV6 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 FE2, ZN, CL, BCL, BPH, U10 and LDA as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.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://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:36:46 2007''

Latest revision as of 09:59, 7 February 2024

PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE WITH THE PROTON TRANSFER INHIBITOR ZN2+PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE WITH THE PROTON TRANSFER INHIBITOR ZN2+

Structural highlights

1dv6 is a 6 chain structure with sequence from Cereibacter sphaeroides. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:, , , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RCEL_CERSP The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1dv6, resolution 2.50Å

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