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- PDB-9gvc: Cryo-EM structure of Halothiobacillus neapolitanus alpha-carboxys... -

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Basic information

Entry
Database: PDB / ID: 9gvc
TitleCryo-EM structure of Halothiobacillus neapolitanus alpha-carboxysome T=4 mini-shell containing CTD truncated mutant of CsoSCA
Components
  • Carboxysome shell vertex protein CsoS4A
  • Major carboxysome shell protein CsoS1A
KeywordsSTRUCTURAL PROTEIN / Carboxysome / carbonic anhydrase
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation
Similarity search - Function
Carboxysome shell vertex protein CsoS4A / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment vertex (BMV) domain profile. / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. ...Carboxysome shell vertex protein CsoS4A / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment vertex (BMV) domain profile. / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily
Similarity search - Domain/homology
Carboxysome shell vertex protein CsoS4A / Major carboxysome shell protein CsoS1A
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.82 Å
AuthorsNg, P.C. / Basle, A. / Liu, L.N. / Marles-Wright, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) 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
DepositionSep 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Oct 8, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
4: Carboxysome shell vertex protein CsoS4A
C: Major carboxysome shell protein CsoS1A
D: Major carboxysome shell protein CsoS1A
E: Major carboxysome shell protein CsoS1A


Theoretical massNumber of molelcules
Total (without water)38,8214
Polymers38,8214
Non-polymers00
Water54030
1
4: Carboxysome shell vertex protein CsoS4A
C: Major carboxysome shell protein CsoS1A
D: Major carboxysome shell protein CsoS1A
E: Major carboxysome shell protein CsoS1A
x 60


Theoretical massNumber of molelcules
Total (without water)2,329,243240
Polymers2,329,243240
Non-polymers00
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Carboxysome shell vertex protein CsoS4A


Mass: 8900.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria)
Gene: csoS4A, orfA, Hneap_0918
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
References: UniProt: O85043
#2: Protein Major carboxysome shell protein CsoS1A


Mass: 9973.478 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria)
Gene: csoS1A, csoS1, Hneap_0915
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
References: UniProt: P45689
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
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: alpha-carboxysome mini shell construct / Type: COMPLEX / Details: T=4 mini shell / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 2.33 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
110 mMTris-HydrochlorideTris-HCl1
21 mMEthylenediaminetetraacetic AcidEDTA1
310 mMMagnesium chlorideMgCl21
420 mMSodium bicarbonateNaHCO31
SpecimenConc.: 3 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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9998

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2EPUimage acquisition
4cryoSPARC4.6.0CTF correction
8PHENIXmodel refinement
10cryoSPARC4.6.0initial Euler assignment
11cryoSPARC4.4final Euler assignment
13cryoSPARC4.33D reconstruction
CTF correctionDetails: Patch CTF in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1752831 / Details: Blob picker with particle diameter 200 - 250 A
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 1.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47086 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032620
ELECTRON MICROSCOPYf_angle_d0.5023554
ELECTRON MICROSCOPYf_dihedral_angle_d4.45383
ELECTRON MICROSCOPYf_chiral_restr0.043429
ELECTRON MICROSCOPYf_plane_restr0.004465

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