2JQR

Solution model of crosslinked complex of cytochrome c and adrenodoxin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy

Xu, X.Reinle, W.Hannemann, F.Konarev, P.V.Svergun, D.I.Bernhardt, R.Ubbink, M.

(2008) J.Am.Chem.Soc. 130: 6395-6403

  • DOI: 10.1021/ja7101357

  • PubMed Abstract: 
  • In the general view of protein-complex formation, a transient and dynamic encounter complex proceeds to form a more stable, well-defined, and active form. In weak protein complexes, however, the encounter state can represent a significant population ...

    In the general view of protein-complex formation, a transient and dynamic encounter complex proceeds to form a more stable, well-defined, and active form. In weak protein complexes, however, the encounter state can represent a significant population of the complex. The redox proteins adrenodoxin (Adx) and cytochrome c (C c) associate to form such a weak and short-lived complex, which is nevertheless active in electron transfer. To study the conformational freedom within the protein complex, the native complex has been compared to a cross-linked counterpart by using solution scattering and NMR spectroscopy. Oligomerization behavior of the native complex in solution revealed by small-angle X-ray scattering indicates a stochastic nature of complex formation. For the cross-linked complex, interprotein paramagnetic effects are observed, whereas for the native complex, extensive averaging occurs, consistent with multiple orientations of the proteins within the complex. Simulations show that C c samples about half of the surface area of adrenodoxin. It is concluded that the complex of Adx/C c is entirely dynamic and can be considered as a pure encounter complex.


    Related Citations: 
    • New aspects of electron transfer revealed by the crystal structure of a truncated bovine adrenodoxin, Adx(4-108)
      Muller, A.,Muller, J.J.,Muller, Y.A.,Uhlmann, H.,Bernhardt, R.,Heinemann, U.
      (1998) Structure 6: 269
    • High-resolution refinement of yeast iso-1-cytochrome C and comparisons with other eukaryotic cytochromes C
      Louie, G.V.,Brayer, G.D.
      (1990) J.Mol.Biol. 214: 527


    Organizational Affiliation

    Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c iso-1
A
108Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 2 
Gene Names: CYC1
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CYC1
Go to UniProtKB:  P00044
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Adrenodoxin, mitochondrial
B
105Bos taurusMutation(s): 2 
Gene Names: FDX1 (ADX)
Find proteins for P00257 (Bos taurus)
Go to Gene View: FDX1
Go to UniProtKB:  P00257
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download SDF File 
Download CCD File 
B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 2JQR Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance