4WT3 | pdb_00004wt3

The N-terminal domain of Rubisco Accumulation Factor 1 from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb4WT3/pdb

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


• Deposited: 2014-10-29 Released: 2015-07-22 
• Deposition Author(s): Hauser, T., Bhat, J.Y., Milicic, G., Wendler, P., Hartl, F.U., Bracher, A., Hayer-Hartl, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.246 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Structure and mechanism of the Rubisco-assembly chaperone Raf1.

Hauser, T., Bhat, J.Y., Milicic, G., Wendler, P., Hartl, F.U., Bracher, A., Hayer-Hartl, M.

(2015) Nat Struct Mol Biol 22: 720-728

• PubMed: 26237510 
• DOI: https://doi.org/10.1038/nsmb.3062
• Primary Citation Related Structures: 
  4WT3, 4WT4, 4WT5


• PubMed Abstract: 
  

  Biogenesis of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits, requires assembly chaperones. Here we analyzed the role of Rubisco accumulation factor1 (Raf1), a dimer of ∼40-kDa subunits. We find that Raf1 from Synechococcus elongatus acts downstream of chaperonin-assisted RbcL folding by stabilizing RbcL antiparallel dimers for assembly into RbcL8 complexes with four Raf1 dimers bound. Raf1 displacement by RbcS results in holoenzyme formation. Crystal structures show that Raf1 from Arabidopsis thaliana consists of a β-sheet dimerization domain and a flexibly linked α-helical domain. Chemical cross-linking and EM reconstruction indicate that the β-domains bind along the equator of each RbcL2 unit, and the α-helical domains embrace the top and bottom edges of RbcL2. Raf1 fulfills a role similar to that of the assembly chaperone RbcX, thus suggesting that functionally redundant factors ensure efficient Rubisco biogenesis.

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Organizational Affiliation: 
• Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, 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: 24 kDa 
• Atom Count: 1,630 
• Modeled Residue Count: 198 
• Deposited Residue Count: 213 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubisco Accumulation Factor 1, isoform 2	A	213	Arabidopsis thaliana	Mutation(s): 0  Gene Names: RAF2, At3g04550, F7O18.2
UniProt
Find proteins for Q9SR19 (Arabidopsis thaliana) Explore Q9SR19  Go to UniProtKB:  Q9SR19

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.246 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.769	α = 90
b = 29.769	β = 90
c = 457.085	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
SHELX	phasing
RESOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-22 
Deposition Author(s): Hauser, T., Bhat, J.Y., Milicic, G., Wendler, P., Hartl, F.U., Bracher, A., Hayer-Hartl, M.

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2015-08-12
  Changes: Database references
• Version 1.2: 2015-09-16
  Changes: Database references
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references