Crystal structure of AtRbcX2 from Arabidopsis thaliana

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

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Insights into eukaryotic Rubisco assembly - Crystal structures of RbcX chaperones from Arabidopsis thaliana.

Kolesinski, P.Golik, P.Grudnik, P.Piechota, J.Markiewicz, M.Tarnawski, M.Dubin, G.Szczepaniak, A.

(2013) Biochim Biophys Acta 1830: 2899-2906

  • DOI: https://doi.org/10.1016/j.bbagen.2012.12.025
  • Primary Citation of Related Structures:  
    4GR2, 4GR6

  • PubMed Abstract: 

    Chloroplasts were formed by uptake of cyanobacteria into eukaryotic cells ca. 1.6 billion years ago. During evolution most of the cyanobacterial genes were transferred from the chloroplast to the nuclear genome. The rbcX gene, encoding an assembly chaperone required for Rubisco biosynthesis in cyanobacteria, was duplicated. Here we demonstrate that homologous eukaryotic chaperones (AtRbcX1 and AtRbcX2) demonstrate different affinities for the C-terminus of Rubisco large subunit and determine their crystal structures. Three-dimensional structures of AtRbcX1 and AtRbcX2 were resolved by the molecular replacement method. Equilibrium binding constants of the C-terminal RbcL peptide by AtRbcX proteins were determined by spectrofluorimetric titration. The binding mode of RbcX-RbcL was predicted using molecular dynamic simulation. We provide crystal structures of both chaperones from Arabidopsis thaliana providing the first structural insight into Rubisco assembly chaperones form higher plants. Despite the low sequence homology of eukaryotic and cyanobacterial Rubisco chaperones the eukaryotic counterparts exhibit surprisingly high similarity of the overall fold to previously determined prokaryotic structures. Modeling studies demonstrate that the overall mode of the binding of RbcL peptide is conserved among these proteins. As such, the evolution of RbcX chaperones is another example of maintaining conserved structural features despite significant drift in the primary amino acid sequence. The presented results are the approach to elucidate the role of RbcX proteins in Rubisco assembly in higher plants.

  • Organizational Affiliation

    Laboratory of Biophysics, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
126Arabidopsis thalianaMutation(s): 1 
Gene Names: At5g19855
Find proteins for Q8L9X2 (Arabidopsis thaliana)
Explore Q8L9X2 
Go to UniProtKB:  Q8L9X2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8L9X2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EDO

Download Ideal Coordinates CCD File 
C [auth B]1,2-ETHANEDIOL
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.77α = 90
b = 63.3β = 96.57
c = 57.32γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHENIXmodel building
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description