9F0H | pdb_00009f0h

cryo-EM structure of carboxysomal mini-shell icosahedral assembly from co-expression of CsoS1C, CsoS4A, and CsoS2-C (T = 9)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Molecular principles of the assembly and construction of a carboxysome shell.

Wang, P.Li, J.Li, T.Li, K.Ng, P.C.Wang, S.Chriscoli, V.Basle, A.Marles-Wright, J.Zhang, Y.Z.Liu, L.N.

(2024) Sci Adv 10: eadr4227-eadr4227

  • DOI: https://doi.org/10.1126/sciadv.adr4227
  • Primary Citation of Related Structures:  
    8YVC, 8YVD, 8YVE, 8YVF, 8YVI, 8YXU, 9F0H

  • PubMed Abstract: 

    Intracellular compartmentalization enhances biological reactions, crucial for cellular function and survival. An example is the carboxysome, a bacterial microcompartment for CO 2 fixation. The carboxysome uses a polyhedral protein shell made of hexamers, pentamers, and trimers to encapsulate Rubisco, increasing CO 2 levels near Rubisco to enhance carboxylation. Despite their role in the global carbon cycle, the molecular mechanisms behind carboxysome shell assembly remain unclear. Here, we present a structural characterization of α-carboxysome shells generated from recombinant systems, which contain all shell proteins and the scaffolding protein CsoS2. Atomic-resolution cryo-electron microscopy of the shell assemblies, with a maximal size of 54 nm, unveil diverse assembly interfaces between shell proteins, detailed interactions of CsoS2 with shell proteins to drive shell assembly, and the formation of heterohexamers and heteropentamers by different shell protein paralogs, facilitating the assembly of larger empty shells. Our findings provide mechanistic insights into the construction principles of α-carboxysome shells and the role of CsoS2 in governing α-carboxysome assembly and functionality.


  • Organizational Affiliation
    • MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.

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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxysome shell protein CsoS1C98Halothiobacillus neapolitanusMutation(s): 0 
Gene Names: csoS1COrf1Hneap_0916
UniProt
Find proteins for P45688 (Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
Explore P45688 
Go to UniProtKB:  P45688
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45688
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxysome assembly protein CsoS2BJ [auth X],
K [auth Z]
279Halothiobacillus neapolitanusMutation(s): 0 
Gene Names: csoS2Hneap_0920
UniProt
Find proteins for O85041 (Halothiobacillus neapolitanus (strain ATCC 23641 / c2))
Explore O85041 
Go to UniProtKB:  O85041
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO85041
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
L [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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
Leverhulme TrustUnited KingdomRPG-2021-286
Royal SocietyUnited KingdomURFR180030

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release