7C2B

Crystal structure of ferredoxin: thioredoxin reductase and thioredoxin f2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for thioredoxin isoform-based fine-tuning of ferredoxin-thioredoxin reductase activity.

Juniar, L.Tanaka, H.Yoshida, K.Hisabori, T.Kurisu, G.

(2020) Protein Sci 29: 2538-2545

  • DOI: https://doi.org/10.1002/pro.3964
  • Primary Citation of Related Structures:  
    7BZK, 7C2B, 7C3F, 7C65

  • PubMed Abstract: 

    Photosynthetic electron transport occurs on the thylakoid membrane of chloroplasts. Ferredoxin (Fd), the final acceptor in the electron transport chain, distributes electrons to several Fd-dependent enzymes including Fd-thioredoxin reductase (FTR). A cascade from Fd to FTR further reduces Thioredoxin (Trx), which tunes the activity of target metabolic enzymes eventually in a light-dependent manner. We previously reported that 10 Trx isoforms in Arabidopsis thaliana can be clustered into three classes based on the kinetics of the FTR-dependent reduction (high-, middle-, and low-efficiency classes). In this study, we determined the X-ray structure of three electron transfer complexes of FTR and Trx isoform, Trx-y1, Trx-f2, and Trx-m2, as representative examples of each class. Superposition of the FTR structure with/without Trx showed no main chain structural changes upon complex formation. There was no significant conformational change for single and complexed Trx-m structures. Nonetheless, the interface of FTR:Trx complexes displayed significant variation. Comparative analysis of the three structures showed two types of intermolecular interactions; (i) common interactions shared by all three complexes and (ii) isoform-specific interactions, which might be important for fine-tuning FTR:Trx activity. Differential electrostatic potentials of Trx isoforms may be key to isoform-specific interactions.


  • Organizational Affiliation

    Institute for Protein Research, Osaka University, Suita, Osaka, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic115Arabidopsis thalianaMutation(s): 0 
Gene Names: FTRC
EC: 1.8.7.2
UniProt
Find proteins for Q9SJ89 (Arabidopsis thaliana)
Explore Q9SJ89 
Go to UniProtKB:  Q9SJ89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SJ89
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin-thioredoxin reductase variable chain, chloroplastic112Arabidopsis thalianaMutation(s): 0 
Gene Names: FTRA2ferredoxinAt5g08410At5g08410/F8L15_140C24_LOCUS21561F8L15.14
UniProt
Find proteins for Q8LBP6 (Arabidopsis thaliana)
Explore Q8LBP6 
Go to UniProtKB:  Q8LBP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8LBP6
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin F2, chloroplastic115Arabidopsis thalianaMutation(s): 1 
Gene Names: At5g16400MQK4.13
UniProt
Find proteins for Q9XFH9 (Arabidopsis thaliana)
Explore Q9XFH9 
Go to UniProtKB:  Q9XFH9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XFH9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
D [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
S [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.738α = 90
b = 83.943β = 90
c = 69.041γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan16H06560

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary