3W5U

Cross-linked complex between Ferredoxin and Ferredoxin-NADP+ reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Concentration-dependent oligomerization of cross-linked complexes between ferredoxin and ferredoxin-NADP(+) reductase

Kimata-Ariga, Y.Kubota-Kawai, H.Lee, Y.-H.Muraki, N.Ikegami, T.Kurisu, G.Hase, T.

(2013) Biochem Biophys Res Commun 434: 867-872

  • DOI: https://doi.org/10.1016/j.bbrc.2013.04.033
  • Primary Citation of Related Structures:  
    3W5U, 3W5V

  • PubMed Abstract: 

    Ferredoxin-NADP(+) reductase (FNR) forms a 1:1 complex with ferredoxin (Fd), and catalyzes the electron transfer between Fd and NADP(+). In our previous study, we prepared a series of site-specifically cross-linked complexes of Fd and FNR, which showed diverse electron transfer properties. Here, we show that X-ray crystal structures of the two different Fd-FNR cross-linked complexes form oligomers by swapping Fd and FNR moieties across the molecules; one complex is a dimer from, and the other is a successive multimeric form. In order to verify whether these oligomeric structures are formed only in crystal, we investigated the possibility of the oligomerization of these complexes in solution. The mean values of the particle size of these cross-linked complexes were shown to increase with the rise of protein concentration at sub-milimolar order, whereas the size of dissociable wild-type Fd:FNR complex was unchanged as analyzed by dynamic light scattering measurement. The oligomerization products were detected by SDS-PAGE after chemical cross-linking of these complexes at the sub-milimolar concentrations. The extent and concentration-dependent profile of the oligomerizaion were differentiated between the two cross-linked complexes. These results show that these Fd-FNR cross-linked complexes exhibit concentration-dependent oligomerization, possibly through swapping of Fd and FNR moieties also in solution. These findings lead to the possibility that some native multi-domain proteins may present similar phenomenon in vivo.


  • Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. a-yoko@protein.osaka-u.ac.jp


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin
A, C, E, G
314Zea maysMutation(s): 1 
Gene Names: L-FNRIZEAMMB73_343560
EC: 1.18.1.2
UniProt
Find proteins for Q9SLP6 (Zea mays)
Explore Q9SLP6 
Go to UniProtKB:  Q9SLP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SLP6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin-1, chloroplastic
B, D, F, H
98Zea maysMutation(s): 1 
Gene Names: FDX1PFD1
UniProt
Find proteins for P27787 (Zea mays)
Explore P27787 
Go to UniProtKB:  P27787
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27787
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.202α = 90
b = 153.634β = 99.42
c = 100.107γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary