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1dwl

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(New page: 200px<br /><applet load="1dwl" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dwl" /> '''THE FERREDOXIN-CYTOCHROME COMPLEX USING HETE...)
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[[Image:1dwl.gif|left|200px]]<br /><applet load="1dwl" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1dwl" />
 
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'''THE FERREDOXIN-CYTOCHROME COMPLEX USING HETERONUCLEAR NMR AND DOCKING SIMULATION'''<br />
 
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==Overview==
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==The Ferredoxin-Cytochrome complex using heteronuclear NMR and docking simulation==
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The combination of docking algorithms with NMR data has been developed, extensively for the studies of protein-ligand interactions. However, to, extend this development for the studies of protein-protein interactions, the intermolecular NOE constraints, which are needed, are more difficult, to access. In the present work, we describe a new approach that combines, an ab initio docking calculation and the mapping of an interaction site, using chemical shift variation analysis. The cytochrome c553-ferredoxin, complex is used as a model of numerous electron-transfer complexes. The, 15N-labeling of both molecules has been obtained, and the mapping of the, interacting site on each partner, respectively, has been done using HSQC, experiments. 1H and 15N chemical shift analysis defines the area of both, molecules involved in the recognition interface. Models of the complex, were generated by an ab initio docking software, the BiGGER program, (bimolecular complex generation with global evaluation and ranking). This, program generates a population of protein-protein docked geometries ranked, by a scoring function, combining relevant stabilization parameters such as, geometric complementarity surfaces, electrostatic interactions, desolvation energy, and pairwise affinities of amino acid side chains. We, have implemented a new module that includes experimental input (here, NMR, mapping of the interacting site) as a filter to select the accurate, models. Final structures were energy minimized using the X-PLOR software, and then analyzed. The best solution has an interface area (1037.4 A2), falling close to the range of generally observed recognition interfaces, with a distance of 10.0 A between the redox centers.
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<StructureSection load='1dwl' size='340' side='right'caption='[[1dwl]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1dwl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfomicrobium_norvegicum Desulfomicrobium norvegicum] and [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._Hildenborough Desulfovibrio vulgaris str. Hildenborough]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DWL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DWL FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Solution NMR , Theoretical Model</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dwl OCA], [https://pdbe.org/1dwl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dwl RCSB], [https://www.ebi.ac.uk/pdbsum/1dwl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dwl ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/FER1_DESNO FER1_DESNO] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dw/1dwl_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1dwl ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1DWL is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans Desulfovibrio desulfuricans] and [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with SF4 and HEC as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DWL OCA].
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*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
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*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
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==Reference==
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__TOC__
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Heteronuclear NMR and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex., Morelli X, Dolla A, Czjzek M, Palma PN, Blasco F, Krippahl L, Moura JJ, Guerlesquin F, Biochemistry. 2000 Mar 14;39(10):2530-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10704202 10704202]
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</StructureSection>
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[[Category: Desulfovibrio desulfuricans]]
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[[Category: Desulfomicrobium norvegicum]]
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[[Category: Desulfovibrio vulgaris]]
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[[Category: Desulfovibrio vulgaris str. Hildenborough]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Czjzek, M.]]
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[[Category: Czjzek M]]
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[[Category: Guerlesquin, F.]]
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[[Category: Guerlesquin F]]
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[[Category: Morelli, X.]]
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[[Category: Morelli X]]
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[[Category: Palma, P.N.]]
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[[Category: Palma PN]]
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[[Category: HEC]]
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[[Category: SF4]]
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[[Category: docking]]
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[[Category: electron transfer]]
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[[Category: ferredoxin-cytochrome complex]]
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[[Category: heteronuclear nmr]]
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[[Category: model]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:38:24 2007''
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The Ferredoxin-Cytochrome complex using heteronuclear NMR and docking simulation

PDB ID 1dwl

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