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- PDB-9g4t: Beta carbonic anhydrase CsoSCA from the Halothiobacillus neapolit... -

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Basic information

Entry
Database: PDB / ID: 9g4t
TitleBeta carbonic anhydrase CsoSCA from the Halothiobacillus neapolitanus alpha-carboxysome
ComponentsImmunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
KeywordsLYASE / Carbonic anhydrase / Carboxysome / rubisco
Function / homology
Function and homology information


carboxysome / carbon fixation / IgG binding / carbonic anhydrase / carbonate dehydratase activity / extracellular region / metal ion binding
Similarity search - Function
Carboxysome shell carbonic anhydrase / Carboxysome shell carbonic anhydrase, N-terminal / Carboxysome shell carbonic anhydrase, C-terminal / : / : / : / Carboxysome Shell Carbonic Anhydrase, C-terminal / Carboxysome Shell Carbonic Anhydrase, catalytic domain / Carboxysome Shell Carbonic Anhydrase, N-terminal / IgG-binding B ...Carboxysome shell carbonic anhydrase / Carboxysome shell carbonic anhydrase, N-terminal / Carboxysome shell carbonic anhydrase, C-terminal / : / : / : / Carboxysome Shell Carbonic Anhydrase, C-terminal / Carboxysome Shell Carbonic Anhydrase, catalytic domain / Carboxysome Shell Carbonic Anhydrase, N-terminal / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Carboxysome shell carbonic anhydrase / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. 'group G' (bacteria)
Halothiobacillus neapolitanus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.51 Å
AuthorsNg, P.C. / Marles-Wright, J. / Basle, A. / Liu, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)2599456 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structure and encapsulation of carbonic anhydrase within the α-carboxysome.
Authors: Pei Cing Ng / Oluwatobi Adegbite / Tianpei Li / Arnaud Baslé / Jon Marles-Wright / Lu-Ning Liu /
Abstract: Carboxysomes in cyanobacteria and certain proteobacteria enable efficient CO fixation by encapsulating ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase (CA) within a ...Carboxysomes in cyanobacteria and certain proteobacteria enable efficient CO 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 and HCO, supplying elevated levels of CO 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 (CsoSCA). 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 CsoSCA interacts with the CsoS1A shell hexamer and is incorporated into the minishells at the inner surface, independent of the CsoS2 linker protein. CsoSCA truncations suggest nonspecific interactions between CsoSCA and CsoS1A. We further show that 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.
History
DepositionJul 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3602
Polymers68,2941
Non-polymers651
Water00
1
A: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
hetero molecules

A: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
hetero molecules

A: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
hetero molecules

A: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
hetero molecules

A: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
hetero molecules

A: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)410,15812
Polymers409,7666
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

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Components

#1: Antibody Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase / IgG-binding protein G / CsoSCA / Carbonic anhydrase / CA / Carboxysome shell protein CsoS3


Mass: 68294.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria), (gene. exp.) Halothiobacillus neapolitanus (bacteria)
Gene: spg, csoS3, ORF1, Hneap_0919 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P06654, UniProt: O85042, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Carbonic anhydrase complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.409 MDa / Experimental value: NO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMTris/Hydrochloric acidTris/HCl1
2150 mMSodium chlorideNaCl1
31 mMEthylenediaminetetraacetic acidEDTA1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 240000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
2EPUimage acquisition
4cryoSPARC4.5CTF correction
7UCSF ChimeraX1.8model fitting
9cryoSPARC4.5initial Euler assignment
10cryoSPARC4.5final Euler assignment
11cryoSPARC4.5classification
12cryoSPARC4.53D reconstruction
13PHENIX1.21.1model refinement
CTF correctionDetails: Patch CTF in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1390946
Details: Blob picker with 150 A diameter. Picks verified using inspect picks job.
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 435319 / Algorithm: FOURIER SPACE / Details: Homogeneous refinement in cryoSPARC / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: Model fitting using ChimeraX
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 108.76 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00373663
ELECTRON MICROSCOPYf_angle_d0.56214974
ELECTRON MICROSCOPYf_chiral_restr0.04552
ELECTRON MICROSCOPYf_plane_restr0.0036659
ELECTRON MICROSCOPYf_dihedral_angle_d3.6538507

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