7C3F | pdb_00007c3f

Crystal structure of ferredoxin: thioredoxin reductase and thioredoxin m2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.245 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7C3F

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 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.

Macromolecule Content 

  • Total Structure Weight: 294.86 kDa 
  • Atom Count: 18,993 
  • Modeled Residue Count: 2,328 
  • Deposited Residue Count: 2,616 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferredoxin-thioredoxin reductase catalytic chain, chloroplastic
A,
D,
G,
J,
M,
P,
S,
W [auth V]
115Arabidopsis 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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferredoxin-thioredoxin reductase variable chain, chloroplastic
B, E, H, K, N
B, E, H, K, N, Q, T
112Arabidopsis 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
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Thioredoxin M2, chloroplastic
C,
F,
I,
L,
O,
R,
U,
V [auth W]
114Arabidopsis thalianaMutation(s): 1 
Gene Names: TRXM2At4g03520F9H3.15T5L23.1
UniProt
Find proteins for Q9SEU8 (Arabidopsis thaliana)
Explore Q9SEU8 
Go to UniProtKB:  Q9SEU8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SEU8
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
(Subject of Investigation/LOI)

Query on SF4



Download:Ideal Coordinates CCD File
AA [auth D]
DA [auth G]
FA [auth J]
IA [auth M]
LA [auth P]
AA [auth D],
DA [auth G],
FA [auth J],
IA [auth M],
LA [auth P],
NA [auth S],
X [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
BA [auth D]
CA [auth E]
EA [auth G]
GA [auth J]
HA [auth L]
BA [auth D],
CA [auth E],
EA [auth G],
GA [auth J],
HA [auth L],
JA [auth M],
KA [auth O],
MA [auth P],
Y [auth A],
Z [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.245 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.262α = 90
b = 137.209β = 90.21
c = 192.457γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2024-11-06
    Changes: Structure summary