8B0Y | pdb_00008b0y

cryo-EM structure of carboxysomal mini-shell: icosahedral assembly from CsoS4A/1A co-expression (T = 3)

• PDB DOI: https://doi.org/10.2210/pdb8B0Y/pdb
• EM Map EMD-15798: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Halothiobacillus neapolitanus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-08 Released: 2023-08-23 
• Deposition Author(s): Ni, T., Jiang, Q., Liu, L.N., Zhang, P.
• Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.79 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Intrinsically disordered CsoS2 acts as a general molecular thread for alpha-carboxysome shell assembly.

Ni, T., Jiang, Q., Ng, P.C., Shen, J., Dou, H., Zhu, Y., Radecke, J., Dykes, G.F., Huang, F., Liu, L.N., Zhang, P.

(2023) Nat Commun 14: 5512-5512

• PubMed: 37679318 
• DOI: https://doi.org/10.1038/s41467-023-41211-y
• Primary Citation Related Structures: 
  8B0Y, 8B11, 8B12


• PubMed Abstract: 
  

  Carboxysomes are a paradigm of self-assembling proteinaceous organelles found in nature, offering compartmentalisation of enzymes and pathways to enhance carbon fixation. In α-carboxysomes, the disordered linker protein CsoS2 plays an essential role in carboxysome assembly and Rubisco encapsulation. Its mechanism of action, however, is not fully understood. Here we synthetically engineer α-carboxysome shells using minimal shell components and determine cryoEM structures of these to decipher the principle of shell assembly and encapsulation. The structures reveal that the intrinsically disordered CsoS2 C-terminus is well-structured and acts as a universal "molecular thread" stitching through multiple shell protein interfaces. We further uncover in CsoS2 a highly conserved repetitive key interaction motif, [IV]TG, which is critical to the shell assembly and architecture. Our study provides a general mechanism for the CsoS2-governed carboxysome shell assembly and cargo encapsulation and further advances synthetic engineering of carboxysomes for diverse biotechnological applications.

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Organizational Affiliation: 
• Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. [e-mail].
School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China. [e-mail].
Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK. [e-mail].
College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China. [e-mail].
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. [e-mail].
Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK. [e-mail].
Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 180-mer - A120B60 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 28.85 kDa 
• Atom Count: 1,953 
• Modeled Residue Count: 267 
• Deposited Residue Count: 279 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxysome shell vertex protein CsoS4A	A	83	Halothiobacillus neapolitanus	Mutation(s): 0  Gene Names: csoS4A, orfA, Hneap_0918
UniProt
Find proteins for O85043 (Halothiobacillus neapolitanus (strain ATCC 23641 / DSM 15147 / CIP 104769 / NCIMB 8539 / c2)) Explore O85043  Go to UniProtKB:  O85043

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Major carboxysome shell protein CsoS1A	B [auth F], C	98	Halothiobacillus neapolitanus	Mutation(s): 0  Gene Names: csoS1A, csoS1, Hneap_0915
UniProt
Find proteins for P45689 (Halothiobacillus neapolitanus (strain ATCC 23641 / DSM 15147 / CIP 104769 / NCIMB 8539 / c2)) Explore P45689  Go to UniProtKB:  P45689

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.79 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-23 
Deposition Author(s): Ni, T., Jiang, Q., Liu, L.N., Zhang, P.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--

Revision History  

• Version 1.0: 2023-08-23
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Database references, Derived calculations