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- EMDB-54978: Cryo-EM structure of H. neapolitanus CsoSCA C283A/C284A inactive ... -

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Basic information

Entry
Database: EMDB / ID: EMD-54978
TitleCryo-EM structure of H. neapolitanus CsoSCA C283A/C284A inactive mutant, hexamer
Map dataSharpened map from final non-uniform refinement in CryoSPARC. Sharpening B-factor: -72.7 A^2.
Sample
  • Complex: HnCsoSCA_C283A-C284A
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Carboxysome shell carbonic anhydrase
  • Ligand: ZINC ION
  • Ligand: water
KeywordsCarbonic anhydrase / carboxysome / CO2 concentration mechanism / LYASE
Function / homology
Function and homology information


carboxysome / carbon fixation / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...carboxysome / carbon fixation / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / carbonic anhydrase / carbonate dehydratase activity / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane / 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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Carboxysome shell carbonic anhydrase / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus c2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.08 Å
AuthorsGaullier G / Vogiatzi N / Blikstad C
Funding support Sweden, 3 items
OrganizationGrant numberCountry
Swedish Research Council2019-03700_VR Sweden
Formas, a Swedish research council for sustainable development2019-01171_Formas Sweden
Swedish Research Council2023-05296_VR Sweden
CitationJournal: Biorxiv / Year: 2026
Title: Molecular mechanism of redox regulation of the alpha-carboxysomal carbonic anhydrase CsoSCA
Authors: Vogiatzi N / Gaullier G / Leufstadius J / Andersson T / Scherbauer T / Blikstad C
History
DepositionSep 2, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54978.png

Downloads & links

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Map

FileDownload / File: emd_54978.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from final non-uniform refinement in CryoSPARC. Sharpening B-factor: -72.7 A^2.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 480 pix.
= 312. Å		0.65 Å/pix.
x 480 pix.
= 312. Å		0.65 Å/pix.
x 480 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.46726432 - 0.7887311
Average (Standard dev.)0.00038911594 (±0.017430814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54978_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_54978_msk_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Mask #3

Fileemd_54978_msk_3.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: Half-map A from final non-uniform refinement in CryoSPARC.

Fileemd_54978_half_map_1.map
AnnotationHalf-map A from final non-uniform refinement in CryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B from final non-uniform refinement in CryoSPARC.

Fileemd_54978_half_map_2.map
AnnotationHalf-map B from final non-uniform refinement in CryoSPARC.
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : HnCsoSCA_C283A-C284A

EntireName: HnCsoSCA_C283A-C284A
Components
  • Complex: HnCsoSCA_C283A-C284A
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Carboxysome shell carbonic anhydrase
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: HnCsoSCA_C283A-C284A

SupramoleculeName: HnCsoSCA_C283A-C284A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Halothiobacillus neapolitanus c2 (bacteria)
Molecular weightTheoretical: 611.1651 KDa

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Carboxysome shel...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Carboxysome shell carbonic anhydrase
type: protein_or_peptide / ID: 1
Details: Double mutation C283A, C284A, engineered to test redox dependence. This is a fusion protein with an N-terminal Strep-MBP tag and a TEV protease site between the MBP tag and CsoSCA. The MBP ...Details: Double mutation C283A, C284A, engineered to test redox dependence. This is a fusion protein with an N-terminal Strep-MBP tag and a TEV protease site between the MBP tag and CsoSCA. The MBP tag and the disordered N-terminus of CsoSCA are not visible in the map.,Double mutation C283A, C284A, engineered to test redox dependence. This is a fusion protein with an N-terminal Strep-MBP tag and a TEV protease site between the MBP tag and CsoSCA. The MBP tag and the disordered N-terminus of CsoSCA are not visible in the map.
Number of copies: 2 / Enantiomer: LEVO / EC number: carbonic anhydrase
Source (natural)Organism: Halothiobacillus neapolitanus c2 (bacteria)
Molecular weightTheoretical: 101.980648 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MWSHPQFEKG SSMKIEEGKL VIWINGDKGY NGLAEVGKKF EKDTGIKVTV EHPDKLEEKF PQVAATGDGP DIIFWAHDRF GGYAQSGLL AEITPDKAFQ DKLYPFTWDA VRYNGKLIAY PIAVEALSLI YNKDLLPNPP KTWEEIPALD KELKAKGKSA L MFNLQEPY ...String:
MWSHPQFEKG SSMKIEEGKL VIWINGDKGY NGLAEVGKKF EKDTGIKVTV EHPDKLEEKF PQVAATGDGP DIIFWAHDRF GGYAQSGLL AEITPDKAFQ DKLYPFTWDA VRYNGKLIAY PIAVEALSLI YNKDLLPNPP KTWEEIPALD KELKAKGKSA L MFNLQEPY FTWPLIAADG GYAFKYENGK YDIKDVGVDN AGAKAGLTFL VDLIKNKHMN ADTDYSIAEA AFNKGETAMT IN GPWAWSN IDTSKVNYGV TVLPTFKGQP SKPFVGVLSA GINAASPNKE LAKEFLENYL LTDEGLEAVN KDKPLGAVAL KSY EEELAK DPRIAATMEN AQKGEIMPNI PQMSAFWYAV RTAVINAASG RQTVDEALKD AQTNSSSNNN NNNNNNNLGI EENL YFQSN ANTRNTRSKQ RAPFGVSSSV KPRLDLIEQA PNPAYDRHPA CITLPERTCR HPLTDLEANE QLGRCEDSVK NRFDR VIPF LQVVAGIPLG LDYVTRVQEL AQSSLGHTLP EELLKDNWIS GHNLKGIFGY ATAKALTAAT EQFSRKIMSE KDDSAS AIG FFLDCGFHAV DISPCADGRL KGLLPYILRL PLTAFTYRKA YAGSMFDIED DLAQWEKNEL RRYREGVPNT ADQPTRY LK IAVYHFSTSD PTHSGCAAHG SNDRAALEAA LTQLMKFREA VENAHAAGAS IDILLIGVDT DTDAIRVHIP DSKGFLNP Y RYVDNTVTYA QTLHLAPDEA RVIIHEAILN ANRSDGWAKG NGVASEGMRR FIGQLLINNL SQIDYVVNRH GGRYPPNDI GHAERYISVG DGFDEVQIRN LAYYAHLDTV EENAIDVDVG IKIFTKLNLS RGLPIPIAIH YRYDPNVPGS RERTVVKARR IYNAIKERF SSLDEQNLLQ FRLSVQAQDI GSPIEEVASA

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Carboxysome shell carbonic anhydrase

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Macromolecule #2: ZINC ION

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

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 253 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.428 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMsodium chlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.04 kPa
Details: Performed with a Pelco easiGlow with a current of 20 mA.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: 4C, 100% relative humidity, delay time 0s, blot time 3s, blot force 0.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 10000 / Average exposure time: 1.6 sec. / Average electron dose: 68.973 e/Å2
Electron beamAcceleration voltage: 300 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: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 497507
Details: Particles were picked with topaz, trained with a set of about 1000 particles picked manually from micrographs denoised by CryoSPARC. Topaz was trained and applied on raw micrographs.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Ab initio reconstruction from the data, using the SGD-based job in CryoSPARC.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 356128
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7) / Details: Non-uniform refinement in CryoSPARC.
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.7)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2-f1


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-9skx:
Cryo-EM structure of H. neapolitanus CsoSCA C283A/C284A inactive mutant, hexamer

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