6KKN

Crystal structure of RuBisCO accumulation factor Raf1 from Anabaena sp. PCC 7120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

Starting Models: experimental
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This is version 1.2 of the entry. See complete history


Literature

Molecular basis for the assembly of RuBisCO assisted by the chaperone Raf1.

Xia, L.Y.Jiang, Y.L.Kong, W.W.Sun, H.Li, W.F.Chen, Y.Zhou, C.Z.

(2020) Nat Plants 6: 708-717

  • DOI: https://doi.org/10.1038/s41477-020-0665-8
  • Primary Citation of Related Structures:  
    6KKM, 6KKN, 6LRR, 6LRS

  • PubMed Abstract: 

    The folding and assembly of RuBisCO, the most abundant enzyme in nature, needs a series of chaperones, including the RuBisCO accumulation factor Raf1, which is highly conserved in cyanobacteria and plants. Here, we report the crystal structures of Raf1 from cyanobacteria Anabaena sp. PCC 7120 and its complex with RuBisCO large subunit RbcL. Structural analyses and biochemical assays reveal that each Raf1 dimer captures an RbcL dimer, with the C-terminal tail inserting into the catalytic pocket, and further mediates the assembly of RbcL dimers to form the octameric core of RuBisCO. Furthermore, the cryo-electron microscopy structures of the RbcL-Raf1-RbcS assembly intermediates enable us to see a dynamic assembly process from RbcL 8 Raf1 8 to the holoenzyme RbcL 8 RbcS 8 . In vitro assays also indicate that Raf1 can attenuate and reverse CcmM-mediated cyanobacterial RuBisCO condensation. Combined with previous findings, we propose a putative model for the assembly of cyanobacterial RuBisCO coordinated by the chaperone Raf1.


  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
All5250 protein376Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: all5250
UniProt
Find proteins for Q8YLP6 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore Q8YLP6 
Go to UniProtKB:  Q8YLP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YLP6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.74α = 90
b = 94.74β = 90
c = 117.98γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2018YFA0903100
Ministry of Science and Technology (China)China2016YFA0400900
National Natural Science Foundation of ChinaChina31630001
National Natural Science Foundation of ChinaChina31621002
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description