6EKB

Crystal structure of the BSD2 homolog of Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb6EKB/pdb

• Classification: CHAPERONE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-26 Released: 2017-12-06 
• Deposition Author(s): Aigner, H., Wilson, R.H., Bracher, A., Calisse, L., Bhat, J.Y., Hartl, F.U., Hayer-Hartl, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

Literature

Plant RuBisCo assembly in E. coli with five chloroplast chaperones including BSD2.

Aigner, H., Wilson, R.H., Bracher, A., Calisse, L., Bhat, J.Y., Hartl, F.U., Hayer-Hartl, M.

(2017) Science 358: 1272-1278

• PubMed: 29217567 
• DOI: https://doi.org/10.1126/science.aap9221
• Primary Citation of Related Structures:  
  6EKB, 6EKC


• PubMed Abstract: 
  

  Plant RuBisCo, a complex of eight large and eight small subunits, catalyzes the fixation of CO ₂ in photosynthesis. The low catalytic efficiency of RuBisCo provides strong motivation to reengineer the enzyme with the goal of increasing crop yields. However, genetic manipulation has been hampered by the failure to express plant RuBisCo in a bacterial host. We achieved the functional expression of Arabidopsis thaliana RuBisCo in Escherichia coli by coexpressing multiple chloroplast chaperones. These include the chaperonins Cpn60/Cpn20, RuBisCo accumulation factors 1 and 2, RbcX, and bundle-sheath defective-2 (BSD2). Our structural and functional analysis revealed the role of BSD2 in stabilizing an end-state assembly intermediate of eight RuBisCo large subunits until the small subunits become available. The ability to produce plant RuBisCo recombinantly will facilitate efforts to improve the enzyme through mutagenesis.

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Organizational Affiliation: 

Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.

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: 8.55 kDa 
• Atom Count: 464 
• Modelled Residue Count: 62 
• Deposited Residue Count: 81 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DnaJ/Hsp40 cysteine-rich domain superfamily protein	A	81	Arabidopsis thaliana	Mutation(s): 0  Gene Names: F1P2.200, At3g47650
UniProt
Find proteins for Q9SN73 (Arabidopsis thaliana) Explore Q9SN73  Go to UniProtKB:  Q9SN73

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.708	α = 90
b = 55.708	β = 90
c = 48.131	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
SHELXDE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Aigner, H., Wilson, R.H., Bracher, A., Calisse, L., Bhat, J.Y., Hartl, F.U., Hayer-Hartl, M.

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2017-12-20
  Changes: Database references