6Z1D | pdb_00006z1d

Crystal structure of the AAA domain of Rubisco Activase from Nostoc sp. (strain PCC 7120), Gadolinium complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 
    0.259 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Dual Functions of a Rubisco Activase in Metabolic Repair and Recruitment to Carboxysomes.

Flecken, M.Wang, H.Popilka, L.Hartl, F.U.Bracher, A.Hayer-Hartl, M.

(2020) Cell 183: 457-473.e20

  • DOI: https://doi.org/10.1016/j.cell.2020.09.010
  • Primary Citation Related Structures: 
    6HAS, 6Z1D, 6Z1E, 6Z1F, 6Z1G

  • PubMed Abstract: 

    Rubisco, the key enzyme of CO 2 fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone Rubisco activase (Rca) in a process that is not well understood. Here, we performed a structural and mechanistic analysis of cyanobacterial Rca, a close homolog of plant Rca. In the Rca:Rubisco complex, Rca is positioned over the Rubisco catalytic site under repair and pulls the N-terminal tail of the large Rubisco subunit (RbcL) into the hexamer pore. Simultaneous displacement of the C terminus of the adjacent RbcL opens the catalytic site for inhibitor release. An alternative interaction of Rca with Rubisco is mediated by C-terminal domains that resemble the small Rubisco subunit. These domains, together with the N-terminal AAA+ hexamer, ensure that Rca is packaged with Rubisco into carboxysomes. The cyanobacterial Rca is a dual-purpose protein with functions in Rubisco repair and carboxysome organization.


  • Organizational Affiliation
    • Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

Macromolecule Content 

  • Total Structure Weight: 66.64 kDa 
  • Atom Count: 4,187 
  • Modeled Residue Count: 533 
  • Deposited Residue Count: 580 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase/oxygenase activase
A, B
290Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: rcaalr1533
UniProt
Find proteins for P58555 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P58555 
Go to UniProtKB:  P58555
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58555
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free:  0.259 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.99α = 90
b = 111.99β = 90
c = 283.818γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references