7ZBT

Subtomogram averaging of Rubisco from native Halothiobacillus carboxysomes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and assembly of cargo Rubisco in two native alpha-carboxysomes.

Ni, T.Sun, Y.Burn, W.Al-Hazeem, M.M.J.Zhu, Y.Yu, X.Liu, L.N.Zhang, P.

(2022) Nat Commun 13: 4299-4299

  • DOI: https://doi.org/10.1038/s41467-022-32004-w
  • Primary Citation of Related Structures:  
    7ZBT, 7ZC1

  • PubMed Abstract: 

    Carboxysomes are a family of bacterial microcompartments in cyanobacteria and chemoautotrophs. They encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase catalyzing carbon fixation inside a proteinaceous shell. How Rubisco complexes pack within the carboxysomes is unknown. Using cryo-electron tomography, we determine the distinct 3D organization of Rubisco inside two distant α-carboxysomes from a marine α-cyanobacterium Cyanobium sp. PCC 7001 where Rubiscos are organized in three concentric layers, and from a chemoautotrophic bacterium Halothiobacillus neapolitanus where they form intertwining spirals. We further resolve the structures of native Rubisco as well as its higher-order assembly at near-atomic resolutions by subtomogram averaging. The structures surprisingly reveal that the authentic intrinsically disordered linker protein CsoS2 interacts with Rubiscos in native carboxysomes but functions distinctively in the two α-carboxysomes. In contrast to the uniform Rubisco-CsoS2 association in the Cyanobium α-carboxysome, CsoS2 binds only to the Rubiscos close to the shell in the Halo α-carboxysome. Our findings provide critical knowledge of the assembly principles of α-carboxysomes, which may aid in the rational design and repurposing of carboxysome structures for new functions.


  • Organizational Affiliation

    Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase large chain473Halothiobacillus neapolitanusMutation(s): 0 
Gene Names: cbbLHneap_0922
EC: 4.1.1.39
UniProt
Find proteins for O85040 (Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
Explore O85040 
Go to UniProtKB:  O85040
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO85040
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase small subunit110Halothiobacillus neapolitanusMutation(s): 0 
Gene Names: cbbSrbcSHneap_0921
UniProt
Find proteins for P45686 (Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
Explore P45686 
Go to UniProtKB:  P45686
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45686
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONemClarity
MODEL REFINEMENTUCSF Chimera

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--
Wellcome TrustUnited Kingdom--
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2023-01-18
    Changes: Database references, Refinement description
  • Version 1.2: 2024-07-24
    Changes: Data collection, Refinement description