1DWL

The Ferredoxin-Cytochrome complex using heteronuclear NMR and docking simulation


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 
  • Selection Criteria: COMBINATION OF NMR SHIFT VARIATION AND A SOFT DOCKING ALGORITHM 

  • Method: THEORETICAL MODEL

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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, P.N.Blasco, F.Krippahl, L.Moura, J.J.G.Guerlesquin, F.

(2000) Biochemistry 39: 2530

  • DOI: https://doi.org/10.1021/bi992306s
  • Primary Citation of Related Structures:  
    1DWL

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Unité de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FERREDOXIN I59Desulfomicrobium norvegicumMutation(s): 0 
Gene Names: FDXI
UniProt
Find proteins for P07485 (Desulfomicrobium norvegicum (strain DSM 1741 / NCIMB 8310))
Explore P07485 
Go to UniProtKB:  P07485
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07485
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C55379Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 0 
UniProt
Find proteins for P04032 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P04032 
Go to UniProtKB:  P04032
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04032
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
D [auth B]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 
  • Selection Criteria: COMBINATION OF NMR SHIFT VARIATION AND A SOFT DOCKING ALGORITHM 
  • Method: THEORETICAL MODEL

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-10
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary