5N9Q | pdb_00005n9q

Structure of A. thaliana RCD1(468-567)

• PDB DOI: https://doi.org/10.2210/pdb5N9Q/pdb
• BMRB: 27034

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-27 Released: 2018-03-14 
• Deposition Author(s): Tossavainen, H., Hellman, M., Vainonen, J., Kangasjarvi, J., Permi, P.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 300 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Literature

Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors.

Shapiguzov, A., Vainonen, J.P., Hunter, K., Tossavainen, H., Tiwari, A., Jarvi, S., Hellman, M., Aarabi, F., Alseekh, S., Wybouw, B., Van Der Kelen, K., Nikkanen, L., Krasensky-Wrzaczek, J., Sipari, N., Keinanen, M., Tyystjarvi, E., Rintamaki, E., De Rybel, B., Salojarvi, J., Van Breusegem, F., Fernie, A.R., Brosche, M., Permi, P., Aro, E.M., Wrzaczek, M., Kangasjarvi, J.

(2019) Elife 8

• PubMed: 30767893 
• DOI: https://doi.org/10.7554/eLife.43284
• Primary Citation Related Structures: 
  5N9Q


• PubMed Abstract: 
  

  Reactive oxygen species (ROS)-dependent signaling pathways from chloroplasts and mitochondria merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). RCD1 interacts in vivo and suppresses the activity of the transcription factors ANAC013 and ANAC017, which mediate a ROS-related retrograde signal originating from mitochondrial complex III. Inactivation of RCD1 leads to increased expression of mitochondrial dysfunction stimulon (MDS) genes regulated by ANAC013 and ANAC017. Accumulating MDS gene products, including alternative oxidases (AOXs), affect redox status of the chloroplasts, leading to changes in chloroplast ROS processing and increased protection of photosynthetic apparatus. ROS alter the abundance, thiol redox state and oligomerization of the RCD1 protein in vivo, providing feedback control on its function. RCD1-dependent regulation is linked to chloroplast signaling by 3'-phosphoadenosine 5'-phosphate (PAP). Thus, RCD1 integrates organellar signaling from chloroplasts and mitochondria to establish transcriptional control over the metabolic processes in both organelles.

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Organizational Affiliation: 
• Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
Viikki Plant Science Center, University of Helsinki, Helsinki, Finland.
Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia.
Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.
Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland.
Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany.
Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria.
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
VIB Center for Plant Systems Biology, Ghent, Belgium.
Viikki Metabolomics Unit, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.
Institute of Technology, University of Tartu, Tartu, Estonia.
Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 13.94 kDa 
• Atom Count: 977 
• Modeled Residue Count: 128 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inactive poly [ADP-ribose] polymerase RCD1	A	128	Arabidopsis thaliana	Mutation(s): 0  Gene Names: RCD1, ATP8, CEO1, At1g32230, F3C3.1
UniProt
Find proteins for Q8RY59 (Arabidopsis thaliana) Explore Q8RY59  Go to UniProtKB:  Q8RY59

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 300 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Tossavainen, H., Hellman, M., Vainonen, J., Kangasjarvi, J., Permi, P.

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection
• Version 1.2: 2019-09-25
  Changes: Data collection, Database references
• Version 1.3: 2024-06-19
  Changes: Data collection, Database references