9FWV | pdb_00009fwv

Rubisco in native beta-carboxysomes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Rubisco packaging and stoichiometric composition of the native beta-carboxysome in Synechococcus elongatus PCC7942.

Sun, Y.Sheng, Y.Ni, T.Ge, X.Sarsby, J.Brownridge, P.J.Li, K.Hardenbrook, N.Dykes, G.F.Rockliffe, N.Eyers, C.E.Zhang, P.Liu, L.N.

(2024) Plant Physiol 197

  • DOI: https://doi.org/10.1093/plphys/kiae665
  • Primary Citation of Related Structures:  
    9FWV

  • PubMed Abstract: 

    Carboxysomes are anabolic bacterial microcompartments that play an essential role in CO2 fixation in cyanobacteria. This self-assembling proteinaceous organelle uses a polyhedral shell constructed by hundreds of shell protein paralogs to encapsulate the key CO2-fixing enzymes Rubisco and carbonic anhydrase. Deciphering the precise arrangement and structural organization of Rubisco enzymes within carboxysomes is crucial for understanding carboxysome formation and overall functionality. Here, we employed cryoelectron tomography and subtomogram averaging to delineate the 3D packaging of Rubiscos within β-carboxysomes in the freshwater cyanobacterium Synechococcus elongatus PCC7942 grown under low light. Our results revealed that Rubiscos are arranged in multiple concentric layers parallel to the shell within the β-carboxysome lumen. We also detected Rubisco binding with the scaffolding protein CcmM in β-carboxysomes, which is instrumental for Rubisco encapsulation and β-carboxysome assembly. Using Quantification conCATamer-based quantitative MS, we determined the absolute stoichiometric composition of the entire β-carboxysome. This study provides insights into the assembly principles and structural variation of β-carboxysomes, which will aid in the rational design and repurposing of carboxysome nanostructures for diverse bioengineering applications.


  • Organizational Affiliation

    Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxysome assembly protein CcmM
A, B, F, T
86Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
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
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase large chain
C, G, H, I, J
C, G, H, I, J, Q, R, S
442Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
EC: 4.1.1.39
UniProt
Find proteins for Q31NB3 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q31NB3 
Go to UniProtKB:  Q31NB3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ31NB3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase small subunit
D, E, K, L, M
D, E, K, L, M, N, O, P
101Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
UniProt
Find proteins for P04716 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Explore P04716 
Go to UniProtKB:  P04716
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04716
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/V009729/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S003339/1
Royal SocietyUnited KingdomURFR180030
Royal SocietyUnited KingdomRGFEA181061
Leverhulme TrustUnited KingdomRPG-2021-286
Leverhulme TrustUnited KingdomRPG-2019-300
European Research Council (ERC)European Union101021133
Wellcome TrustUnited Kingdom206422/Z/17/Z
National Natural Science Foundation of China (NSFC)China32070109

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release