1dwl

From Proteopedia

(Difference between revisions)

Current revision

The Ferredoxin-Cytochrome complex using heteronuclear NMR and docking simulation

Structural highlights

1dwl is a 2 chain structure with sequence from Desulfomicrobium norvegicum and Desulfovibrio vulgaris str. Hildenborough. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Hybrid , Solution NMR , Theoretical Model, 3 models
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

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

Publication Abstract from PubMed

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.

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:10704202^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Morelli X, Dolla A, Czjzek M, Palma PN, Blasco F, Krippahl L, Moura JJ, Guerlesquin F. Heteronuclear NMR and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex. Biochemistry. 2000 Mar 14;39(10):2530-7. PMID:10704202

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1dwl"

@@ Line 1: / Line 1: @@
 ==The Ferredoxin-Cytochrome complex using heteronuclear NMR and docking simulation==
-<StructureSection load='1dwl' size='340' side='right'caption='[[1dwl]], [[NMR_Ensembles_of_Models | 3 NMR models]]' scene=''>
+<StructureSection load='1dwl' size='340' side='right'caption='[[1dwl]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1dwl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ ] and [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. 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>
+<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>
-</td></tr><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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Solution NMR , Theoretical Model, 3 models</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dvh|1dvh]], [[2dvh|2dvh]], [[1fxd|1fxd]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</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=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>
 </table>
-== Function ==
-[[https://www.uniprot.org/uniprot/FER1_DESNO FER1_DESNO]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. [[https://www.uniprot.org/uniprot/CY553_DESVH CY553_DESVH]] Natural electron acceptor for a formate dehydrogenase.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dw/1dwl_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 37: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Desulfovibrio vulgaris]]
+[[Category: Desulfomicrobium norvegicum]]
+[[Category: Desulfovibrio vulgaris str. Hildenborough]]
 [[Category: Large Structures]]
-[[Category: Czjzek, M]]
+[[Category: Czjzek M]]
-[[Category: Guerlesquin, F]]
+[[Category: Guerlesquin F]]
-[[Category: Morelli, X]]
+[[Category: Morelli X]]
-[[Category: Palma, P N]]
+[[Category: Palma PN]]
-[[Category: Docking]]
-[[Category: Electron transfer]]
-[[Category: Ferredoxin-cytochrome complex]]
-[[Category: Heteronuclear nmr]]
-[[Category: Model]]

1dwl

From Proteopedia

Current revision

The Ferredoxin-Cytochrome complex using heteronuclear NMR and docking simulation

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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Proteopedia Page Contributors and Editors (what is this?)

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