Skip to main content

 6J13 | pdb_00006j13

Redox protein from Chlamydomonas reinhardtii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.251 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6J13

This is version 1.2 of the entry. See complete history. 

Literature

Calcium sensing via EF-hand 4 enables thioredoxin activity in the sensor-responder protein calredoxin in the green algaChlamydomonas reinhardtii.

Charoenwattanasatien, R., Zinzius, K., Scholz, M., Wicke, S., Tanaka, H., Brandenburg, J.S., Marchetti, G.M., Ikegami, T., Matsumoto, T., Oda, T., Sato, M., Hippler, M., Kurisu, G.

(2020) J Biol Chem 295: 170-180

  • DOI: https://doi.org/10.1074/jbc.RA119.008735
  • Primary Citation Related Structures: 
    6J13

  • PubMed Abstract: 

    Calcium (Ca 2+ ) and redox signaling enable cells to quickly adapt to changing environments. The signaling protein calredoxin (CRX) from the green alga Chlamydomonas reinhardtii is a chloroplast-resident thioredoxin having Ca 2+ -dependent activity and harboring a unique combination of an EF-hand domain connected to a typical thioredoxin-fold. Using small-angle X-ray scattering (SAXS), FRET, and NMR techniques, we found that Ca 2+ -binding not only induces a conformational change in the EF-hand domain, but also in the thioredoxin domain, translating into the onset of thioredoxin redox activity. Functional analyses of CRX with genetically altered EF-hands revealed that EF-hand 4 is important for mediating the communication between the two domains. Moreover, we crystallized a variant (C174S) of the CRX target protein peroxiredoxin 1 (PRX1) at 2.4 Å resolution, modeled the interaction complex of the two proteins, and analyzed it by cross-linking and MS analyses, revealing that the interaction interface is located close to the active sites of both proteins. Our findings shed light on the Ca 2+ binding-induced changes in CRX structure in solution at the level of the overall protein and individual domains and residues.


  • Organizational Affiliation: 
    • Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita Osaka 565-0871, Japan; Synchrotron Light Research Institute (Public Organization), 30000 Nakhon Ratchasima, Thailand.

Macromolecule Content 

  • Total Structure Weight: 246.93 kDa 
  • Atom Count: 13,006 
  • Modeled Residue Count: 1,631 
  • Deposited Residue Count: 2,210 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2-cys peroxiredoxin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
221Chlamydomonas reinhardtiiMutation(s): 1 
Gene Names: thioredoxin peroxidase
EC: 1.11.1 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt
Find proteins for Q9FE86 (Chlamydomonas reinhardtii)
Explore Q9FE86 
Go to UniProtKB:  Q9FE86
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FE86
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.251 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.99α = 90
b = 419.23β = 90
c = 94.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan16H06560

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description