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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: To Be Published
Title: Cryo-EM structure of Halothiobacillus neapolitanus alpha-carboxysome T=4 mini-shell containing CTD truncated mutant of CsoSCA
Authors: Ng, P.C. / Basle, A. / Liu, L.N. / Marles-Wright, J.
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
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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

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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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