Crystal Structure of the small subunit-like domain 1 of CcmM from Synechococcus elongatus (strain PCC 7942), thiol-oxidized form

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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Rubisco condensate formation by CcmM in beta-carboxysome biogenesis.

Wang, H.Yan, X.Aigner, H.Bracher, A.Nguyen, N.D.Hee, W.Y.Long, B.M.Price, G.D.Hartl, F.U.Hayer-Hartl, M.

(2019) Nature 566: 131-135

  • DOI: https://doi.org/10.1038/s41586-019-0880-5
  • Primary Citation of Related Structures:  
    6HBA, 6HBB, 6HBC

  • PubMed Abstract: 

    Cells use compartmentalization of enzymes as a strategy to regulate metabolic pathways and increase their efficiency 1 . The α- and β-carboxysomes of cyanobacteria contain ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)-a complex of eight large (RbcL) and eight small (RbcS) subunits-and carbonic anhydrase 2-4 . As HCO 3 - can diffuse through the proteinaceous carboxysome shell but CO 2 cannot 5 , carbonic anhydrase generates high concentrations of CO 2 for carbon fixation by Rubisco 6 . The shell also prevents access to reducing agents, generating an oxidizing environment 7-9 . The formation of β-carboxysomes involves the aggregation of Rubisco by the protein CcmM 10 , which exists in two forms: full-length CcmM (M58 in Synechococcus elongatus PCC7942), which contains a carbonic anhydrase-like domain 8 followed by three Rubisco small subunit-like (SSUL) modules connected by flexible linkers; and M35, which lacks the carbonic anhydrase-like domain 11 . It has long been speculated that the SSUL modules interact with Rubisco by replacing RbcS 2-4 . Here we have reconstituted the Rubisco-CcmM complex and solved its structure. Contrary to expectation, the SSUL modules do not replace RbcS, but bind close to the equatorial region of Rubisco between RbcL dimers, linking Rubisco molecules and inducing phase separation into a liquid-like matrix. Disulfide bond formation in SSUL increases the network flexibility and is required for carboxysome function in vivo. Notably, the formation of the liquid-like condensate of Rubisco is mediated by dynamic interactions with the SSUL domains, rather than by low-complexity sequences, which typically mediate liquid-liquid phase separation in eukaryotes 12,13 . Indeed, within the pyrenoids of eukaryotic algae, the functional homologues of carboxysomes, Rubisco adopts a liquid-like state by interacting with the intrinsically disordered protein EPYC1 14 . Understanding carboxysome biogenesis will be important for efforts to engineer CO 2 -concentrating mechanisms in plants 15-19 .

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbon dioxide concentrating mechanism protein CcmM
A, B
92Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: ccmMSynpcc7942_1423
Find proteins for Q03513 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q03513 
Go to UniProtKB:  Q03513
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03513
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.896α = 90
b = 89.185β = 107.7
c = 36.29γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.4: 2019-02-20
    Changes: Data collection, Database references
  • Version 1.5: 2024-01-17
    Changes: Data collection, Database references, Refinement description