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- EMDB-53925: Structure of DabA2B2 complex solved under ambient condition -

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Basic information

Entry
Database: EMDB / ID: EMD-53925
TitleStructure of DabA2B2 complex solved under ambient condition
Map data
Sample
  • Complex: Dissolved inorganic carbon-accumulating complex DabA2B2
    • Protein or peptide: Probable inorganic carbon transporter subunit DabA2
    • Protein or peptide: Probable inorganic carbon transporter subunit DabB2
  • Ligand: ZINC ION
  • Ligand: CARBON DIOXIDE
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: water
KeywordsCarbonic anhydrase / Hydro-lyase / Proton-pumping transporter / Carbon-concentrating mechanism / TRANSPORT PROTEIN
Function / homology
Function and homology information


electron transport coupled proton transport / NADH dehydrogenase activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / zinc ion binding / plasma membrane
Similarity search - Function
Probable inorganic carbon transporter subunit DabA / Probable inorganic carbon transporter subunit DabB / Probable inorganic carbon transporter subunit DabA / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-quinone oxidoreductase, chain 5-like / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM
Similarity search - Domain/homology
Probable inorganic carbon transporter subunit DabA2 / Probable inorganic carbon transporter subunit DabB2
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus c2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLo YK / Bohn S / Schuller J
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHaqU 3364/1-1 Germany
CitationJournal: To Be Published
Title: Structural insights into membrane potential-coupled dissolved inorganic carbon-accumulating complex
Authors: Lo YK / Seletskiy M / Bohn S / Stripp ST / Deobald D / Schuller J
History
DepositionMay 30, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53925.png

Downloads & links

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Map

FileDownload / File: emd_53925.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 340 pix.
= 248.2 Å		0.73 Å/pix.
x 340 pix.
= 248.2 Å		0.73 Å/pix.
x 340 pix.
= 248.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.941109 - 1.2177588
Average (Standard dev.)0.00019803696 (±0.032069255)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 248.20001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53925_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53925_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dissolved inorganic carbon-accumulating complex DabA2B2

EntireName: Dissolved inorganic carbon-accumulating complex DabA2B2
Components
  • Complex: Dissolved inorganic carbon-accumulating complex DabA2B2
    • Protein or peptide: Probable inorganic carbon transporter subunit DabA2
    • Protein or peptide: Probable inorganic carbon transporter subunit DabB2
  • Ligand: ZINC ION
  • Ligand: CARBON DIOXIDE
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
  • Ligand: water

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Supramolecule #1: Dissolved inorganic carbon-accumulating complex DabA2B2

SupramoleculeName: Dissolved inorganic carbon-accumulating complex DabA2B2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Halothiobacillus neapolitanus c2 (bacteria)

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Macromolecule #1: Probable inorganic carbon transporter subunit DabA2

MacromoleculeName: Probable inorganic carbon transporter subunit DabA2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus c2 (bacteria)
Molecular weightTheoretical: 95.988258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTLTSLQRS EAQRNHIVDL IDKACLRIAP IWPLDSFVAV NPYLGLIDQP FDTVGRYLEQ TVGESLFMDH GWFADKIAQG EITDDDLAQ AAQQLDPSIS LDTIKQQLAV HRQPAPALPL VTNELDRRDA PPVSEFVIEQ VSQFMANYYD RGQALWHLPK E ASASLFAQ ...String:
MTTLTSLQRS EAQRNHIVDL IDKACLRIAP IWPLDSFVAV NPYLGLIDQP FDTVGRYLEQ TVGESLFMDH GWFADKIAQG EITDDDLAQ AAQQLDPSIS LDTIKQQLAV HRQPAPALPL VTNELDRRDA PPVSEFVIEQ VSQFMANYYD RGQALWHLPK E ASASLFAQ WRRYTLINRS ASAVGLKQVR QHLLAVPSDA IDALFWALDQ INLPESRLPD YLFTLLKTIG GWASWCRYLH FQ AGLHGES QHDLRDLLII RLVWVALVIK ETSSAGRQQW RAKLNDWFDP AKLVASPSAT ATASTKAQSS RIDEILLAAA EQA FRRRIN AGLNRQPADA PDQQAERPTV QAAFCIDVRS EVFRRHLEAS SPGLETIGFA GFFGLPIDYC RMGESEARLQ NPVL INPAY RAQETGDPAI AQHRHARQSR GAIWKQFKLS AASCFTFVES AGLSYVPRLL ADSLGWHRSS LPPDAPGLTP EERAR LHPQ LVKLDGGALS TQEKVDLAEK VLRGLGLTHT FAPIVLLAGH GSSTTNNPHR AGLDCGACAG QAGDVNARVA VQLLNE AAV RLGLIERGIA IPRDTRFVAA LHDTTTDHIE LLDLDQSGIE SDQLSSLTQA LKQAGELTRL ERLVTLEAQV DTVDAEK QA TFRGRDWSQV RPEWGLAGNA AFIAAPRWRT RGLDLGGRAF LHDYDWRHDK EFGVLNVIMT APLIVANWIN LQYYGSTV D NLHQGAGNKV LHNVVGGTVG VIEGNGGDLR VGLAMQSLHD GEQWRHEPLR LSAYIEAPIA EIDKIIAGHD MLNALINNR WMHILHIDDN GIPHRRHAHG DWRPEPISGS LEVLFQGPGG SAWSHPQFEK GGGSGGGSGG SAWSHPQFEK

UniProtKB: Probable inorganic carbon transporter subunit DabA2

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Macromolecule #2: Probable inorganic carbon transporter subunit DabB2

MacromoleculeName: Probable inorganic carbon transporter subunit DabB2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus c2 (bacteria)
Molecular weightTheoretical: 59.187109 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTIEFSHTTG LLLLAMPALL LMAAVIKPKQ GAAYARAYRQ RVQWTSFAAF GLALLAVVSF LFARQQNLML GAGSLPAGLG LLALSIQVN GLTLVLASLV SFVLSVIARY SVQYLDGDPQ QARFFRLLAV TGGFFLLVVI SGNLGLFTLA IIATGFGLHR L LSFYADRP ...String:
MTIEFSHTTG LLLLAMPALL LMAAVIKPKQ GAAYARAYRQ RVQWTSFAAF GLALLAVVSF LFARQQNLML GAGSLPAGLG LLALSIQVN GLTLVLASLV SFVLSVIARY SVQYLDGDPQ QARFFRLLAV TGGFFLLVVI SGNLGLFTLA IIATGFGLHR L LSFYADRP RAIMATHKKS IFSRTADALL LAATVLIGHQ IGSLEFSQIS AYVHAQDHLS IALHVAAWLI VLAAILKSAQ FP FHGWLIQ VMEAPTPVSA LMHAGVVYSG AIIVLRTSEL LAADGTALLL LALIGLMTLA IGSLVMLTQS AIKSSLAWST AAQ LGFMML ELGLGLFGLA LLHLVGHSLY KAHAFLSSGS MTDHLRQAKV LKNRPISVVA WFTTVIVSGL FTLGIAAAMG LSID QEPML PAVLTIIALA TAQLMLKALS HGTWREILVA AGAAIAMTGV YVFLHEVFIT GFADTLAATP QRAPLLDLLL MAITI ITFL FVAWLQGPGK TLMSPERQFA LFVHLNNGLY LDRWVERLAF RFWPEKVGRA PKKSCAVIPP NPSGIEP

UniProtKB: Probable inorganic carbon transporter subunit DabB2

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: CARBON DIOXIDE

MacromoleculeName: CARBON DIOXIDE / type: ligand / ID: 4 / Number of copies: 6 / Formula: CO2
Molecular weightTheoretical: 44.01 Da
Chemical component information

ChemComp-CO2:
CARBON DIOXIDE

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Macromolecule #5: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...

MacromoleculeName: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
type: ligand / ID: 5 / Number of copies: 4 / Formula: 6OU
Molecular weightTheoretical: 717.996 Da
Chemical component information

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 259 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold prediction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 254703
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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