9GVC | pdb_00009gvc

Cryo-EM structure of Halothiobacillus neapolitanus alpha-carboxysome T=4 mini-shell containing CTD truncated mutant of CsoSCA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and encapsulation of carbonic anhydrase within the alpha-carboxysome.

Ng, P.C.Adegbite, O.Li, T.Basle, A.Marles-Wright, J.Liu, L.N.

(2025) Proc Natl Acad Sci U S A 122: e2523723122-e2523723122

  • DOI: https://doi.org/10.1073/pnas.2523723122
  • Primary Citation of Related Structures:  
    9G4T, 9GVC, 9GW1

  • PubMed Abstract: 

    Carboxysomes in cyanobacteria and certain proteobacteria enable efficient CO 2 fixation by encapsulating ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase (CA) within a semipermeable shell. Sequestered CA catalyze the rapid interconversion of CO 2 and HCO 3 - , supplying elevated levels of CO 2 to boost Rubisco carboxylation. Despite its essential role, the structure and encapsulation of CA within carboxysomes remain poorly understood. Here, we determined the molecular structure of α-carboxysomal CA from the model chemoautotrophic bacterium Halothiobacillus neapolitanus ( Hn CsoSCA). Hn CsoSCA adopts a trimer-of-dimers oligomeric structure without the incorporation of a zinc ion at its symmetric center. Using synthetic minishells, we demonstrate that Hn CsoSCA interacts with the CsoS1A shell hexamer and is incorporated into the minishells at the inner surface, independent of the CsoS2 linker protein. Hn CsoSCA truncations suggest nonspecific interactions between Hn CsoSCA and CsoS1A. We further show that Hn CsoSCA bridges Rubisco and the shell facets. Our study offers insights into the assembly and encapsulation mechanisms of α-carboxysomes and provides the framework for reprogramming carboxysome structures for synthetic biology and biotechnological applications.


  • Organizational Affiliation
    • Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxysome shell vertex protein CsoS4AA [auth 4]83Halothiobacillus neapolitanusMutation(s): 0 
Gene Names: csoS4AorfAHneap_0918
UniProt
Find proteins for O85043 (Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
Explore O85043 
Go to UniProtKB:  O85043
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO85043
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Major carboxysome shell protein CsoS1AB [auth C],
C [auth D],
D [auth E]
98Halothiobacillus neapolitanusMutation(s): 0 
Gene Names: csoS1AcsoS1Hneap_0915
UniProt
Find proteins for P45689 (Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
Explore P45689 
Go to UniProtKB:  P45689
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45689
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Data collection, Database references