1dv3: Difference between revisions

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<StructureSection load='1dv3' size='340' side='right'caption='[[1dv3]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='1dv3' size='340' side='right'caption='[[1dv3]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1dv3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DV3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1dv3]] 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=1DV3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DV3 FirstGlance]. <br>
</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=CD:CADMIUM+ION'>CD</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></td></tr>
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1aig|1aig]], [[1aij|1aij]], [[1ds8|1ds8]], [[1dv6|1dv6]]</div></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=CD:CADMIUM+ION'>CD</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></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=1dv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv3 OCA], [https://pdbe.org/1dv3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dv3 RCSB], [https://www.ebi.ac.uk/pdbsum/1dv3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv3 ProSAT]</span></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=1dv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv3 OCA], [https://pdbe.org/1dv3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dv3 RCSB], [https://www.ebi.ac.uk/pdbsum/1dv3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv3 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RCEL_RHOSH RCEL_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[https://www.uniprot.org/uniprot/RCEH_RHOSH RCEH_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[https://www.uniprot.org/uniprot/RCEM_RHOSH RCEM_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.  
[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.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1dv3 ConSurf].
</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=1dv3 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:10677497<ref>PMID:10677497</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1dv3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Cereibacter sphaeroides]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Rhodobacter sphaeroides]]
[[Category: Abresch EC]]
[[Category: Abresch, E C]]
[[Category: Axelrod HL]]
[[Category: Axelrod, H L]]
[[Category: Feher G]]
[[Category: Feher, G]]
[[Category: Okamura MY]]
[[Category: Okamura, M Y]]
[[Category: Paddock ML]]
[[Category: Paddock, M L]]
[[Category: Bacterial photosynthesis]]
[[Category: Cation binding]]
[[Category: Integral membrane protein]]
[[Category: Metal ion binding]]
[[Category: Photosynthesis]]
[[Category: Proton transfer]]
[[Category: Rhodobacter sphaeroide]]

Latest revision as of 09:59, 7 February 2024

PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-SEPARATED D+QAQB-STATE WITH THE PROTON TRANSFER INHIBITOR CD2+PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-SEPARATED D+QAQB-STATE WITH THE PROTON TRANSFER INHIBITOR CD2+

Structural highlights

1dv3 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.

1dv3, resolution 2.50Å

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