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- EMDB-51067: Beta carbonic anhydrase CsoSCA from the Halothiobacillus neapolit... -

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Basic information

Entry
Database: EMDB / ID: EMD-51067
TitleBeta carbonic anhydrase CsoSCA from the Halothiobacillus neapolitanus alpha-carboxysome
Map dataPrimary map
Sample
  • Complex: Carbonic anhydrase complex
    • Protein or peptide: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
  • Ligand: ZINC ION
KeywordsCarbonic anhydrase / Carboxysome / rubisco / LYASE
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 speciesHalothiobacillus neapolitanus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.51 Å
AuthorsNg PC / Marles-Wright J / Basle A / Liu L
Funding support United Kingdom, 1 items
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, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51067.png

Downloads & links

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Map

FileDownload / File: emd_51067.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 275.507 Å		1.08 Å/pix.
x 256 pix.
= 275.507 Å		1.08 Å/pix.
x 256 pix.
= 275.507 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0762 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.16891192 - 0.48832244
Average (Standard dev.)-0.00026578293 (±0.01924061)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 275.5072 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51067_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_51067_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_51067_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_51067_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Carbonic anhydrase complex

EntireName: Carbonic anhydrase complex
Components
  • Complex: Carbonic anhydrase complex
    • Protein or peptide: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
  • Ligand: ZINC ION

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Supramolecule #1: Carbonic anhydrase complex

SupramoleculeName: Carbonic anhydrase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Molecular weightTheoretical: 409 KDa

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Macromolecule #1: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anh...

MacromoleculeName: Immunoglobulin G-binding protein G,Carboxysome shell carbonic anhydrase
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: carbonic anhydrase
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Molecular weightTheoretical: 68.294305 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK YKLILNGKTL KGETTTEAVD AATAEKVFKQ YANDNGVDGE WTYDDATKTF TVTEPMSDY DIPTTENLYF QGNTRNTRSK QRAPFGVSSS VKPRLDLIEQ APNPAYDRHP ACITLPERTC RHPLTDLEAN E QLGRCEDS ...String:
MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK YKLILNGKTL KGETTTEAVD AATAEKVFKQ YANDNGVDGE WTYDDATKTF TVTEPMSDY DIPTTENLYF QGNTRNTRSK QRAPFGVSSS VKPRLDLIEQ APNPAYDRHP ACITLPERTC RHPLTDLEAN E QLGRCEDS VKNRFDRVIP FLQVVAGIPL GLDYVTRVQE LAQSSLGHTL PEELLKDNWI SGHNLKGIFG YATAKALTAA TE QFSRKIM SEKDDSASAI GFFLDCGFHA VDISPCADGR LKGLLPYILR LPLTAFTYRK AYAGSMFDIE DDLAQWEKNE LRR YREGVP NTADQPTRYL KIAVYHFSTS DPTHSGCAAH GSNDRAALEA ALTQLMKFRE AVENAHCCGA SIDILLIGVD TDTD AIRVH IPDSKGFLNP YRYVDNTVTY AQTLHLAPDE ARVIIHEAIL NANRSDGWAK GNGVASEGMR RFIGQLLINN LSQID YVVN RHGGRYPPND IGHAERYISV GDGFDEVQIR NLAYYAHLDT VEENAIDVDV GIKIFTKLNL SRGLPIPIAI HYRYDP NVP GSRERTVVKA RRIYNAIKER FSSLDEQNLL QFRLSVQAQD IGSPIEEVAS A

UniProtKB: Immunoglobulin G-binding protein G, Carboxysome shell carbonic anhydrase

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMTris/HClTris/Hydrochloric acid
150.0 mMNaClSodium chloride
1.0 mMEDTAEthylenediaminetetraacetic acid
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa
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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 240000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1390946
Details: Blob picker with 150 A diameter. Picks verified using inspect picks job.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Details: Patch CTF in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio asymmetric model / Details: Ab initio job in cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Details: Homogeneous refinement in cryoSPARC / Number images used: 435319
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5) / Details: Homogeneous refinement
Final 3D classificationNumber classes: 2 / Avg.num./class: 200000 / Software - Name: cryoSPARC (ver. 4.5) / Details: 3D classification with 2 classes
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsModel fitting using ChimeraX
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-9g4t:
Beta carbonic anhydrase CsoSCA from the Halothiobacillus neapolitanus alpha-carboxysome

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