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- PDB-9rd0: Structure of DabA2B2 complex solved under ambient condition -

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Basic information

Entry
Database: PDB / ID: 9rd0
TitleStructure of DabA2B2 complex solved under ambient condition
Components(Probable inorganic carbon transporter subunit ...) x 2
KeywordsTRANSPORT PROTEIN / Carbonic anhydrase / Hydro-lyase / Proton-pumping transporter / Carbon-concentrating mechanism
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
Chem-6OU / CARBON DIOXIDE / Probable inorganic carbon transporter subunit DabA2 / Probable inorganic carbon transporter subunit DabB2
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus c2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLo, Y.K. / Bohn, S. / Schuller, J.
Funding support Germany, 1items
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, Y.K. / Seletskiy, M. / Bohn, S. / Stripp, S.T. / Deobald, D. / Schuller, J.
History
DepositionMay 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable inorganic carbon transporter subunit DabA2
B: Probable inorganic carbon transporter subunit DabB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,37713
Polymers155,1752
Non-polymers3,20111
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Probable inorganic carbon transporter subunit ... , 2 types, 2 molecules AB

#1: Protein Probable inorganic carbon transporter subunit DabA2


Mass: 95988.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus c2 (bacteria)
Gene: dabA2, Hneap_0211 / Production host: Escherichia coli (E. coli) / References: UniProt: D0KWS7
#2: Protein Probable inorganic carbon transporter subunit DabB2


Mass: 59187.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus c2 (bacteria)
Gene: dabB2, Hneap_0212 / Production host: Escherichia coli (E. coli) / References: UniProt: D0KWS8

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Non-polymers , 4 types, 270 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-6OU / [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate


Mass: 717.996 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H76NO8P / Comment: phospholipid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: Dissolved inorganic carbon-accumulating complex DabA2B2
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Halothiobacillus neapolitanus c2 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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 defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 254703 / Symmetry type: POINT

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