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- EMDB-51641: Cryo-EM structure of alpha-carboxysome T=4 mini-shell containing ... -

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Basic information

Entry
Database: EMDB / ID: EMD-51641
TitleCryo-EM structure of alpha-carboxysome T=4 mini-shell containing CTD only mutant of CsoSCA
Map dataExperimental map
Sample
  • Complex: T=4 alpha-carboxysome mini-shell
    • Protein or peptide: Carboxysome shell vertex protein CsoS4A
    • Protein or peptide: Major carboxysome shell protein CsoS1A
KeywordsCarboxysome / carbonic anhydrase / STRUCTURAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNg PC / Basle A / Marles-Wright J / Liu L
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of alpha-carboxysome T=4 mini-shell containing CTD only mutant of CsoSCA
Authors: Ng PC / Basle A / Marles-Wright J / Liu L
History
DepositionSep 26, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51641.png

Downloads & links

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Map

FileDownload / File: emd_51641.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationExperimental map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 512 pix.
= 514.304 Å		1 Å/pix.
x 512 pix.
= 514.304 Å		1 Å/pix.
x 512 pix.
= 514.304 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.10230389 - 0.3095321
Average (Standard dev.)-0.000029684277 (±0.015546036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 514.304 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51641_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_51641_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_51641_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_51641_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : T=4 alpha-carboxysome mini-shell

EntireName: T=4 alpha-carboxysome mini-shell
Components
  • Complex: T=4 alpha-carboxysome mini-shell
    • Protein or peptide: Carboxysome shell vertex protein CsoS4A
    • Protein or peptide: Major carboxysome shell protein CsoS1A

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Supramolecule #1: T=4 alpha-carboxysome mini-shell

SupramoleculeName: T=4 alpha-carboxysome mini-shell / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Molecular weightTheoretical: 2.326 MDa

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Macromolecule #1: Carboxysome shell vertex protein CsoS4A

MacromoleculeName: Carboxysome shell vertex protein CsoS4A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Molecular weightTheoretical: 8.900287 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MKIMQVEKTL VSTNRIADMG HKPLLVVWEK PGAPRQVAVD AIGCIPGDWV LCVGSSAARE AAGSKSYPSD LTIIGIIDQW NGE

UniProtKB: Carboxysome shell vertex protein CsoS4A

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Macromolecule #2: Major carboxysome shell protein CsoS1A

MacromoleculeName: Major carboxysome shell protein CsoS1A / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Molecular weightTheoretical: 9.973478 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MADVTGIALG MIETRGLVPA IEAADAMTKA AEVRLVGRQF VGGGYVTVLV RGETGAVNAA VRAGADACER VGDGLVAAHI IARVHSEVE NILPKAPQA

UniProtKB: Major carboxysome shell protein CsoS1A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration7 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMTris-HClTris-Hydrochloride
1.0 mMEDTAEthylenediaminetetraacetic Acid
10.0 mMMCl2Magnesium chloride
20.0 mMNaHCO3Sodium bicarbonate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 240000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 123441
Details: Blob picker with 300 A diameter. Picks verified using inspect picks job.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3) / Details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio / Details: Single icosahedral model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 3003
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3) / Details: Homogeneous refinement
Final 3D classificationNumber classes: 1 / Avg.num./class: 3003 / Software - Name: cryoSPARC (ver. 4.3) / Details: Single 3D class
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8b11


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsModel fitted using ChimeraX manual placement and fit in volume tool.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation
Output model

PDB-9gw1:
Cryo-EM structure of alpha-carboxysome T=4 mini-shell containing CTD only mutant of CsoSCA

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