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- PDB-38rh: Structure of the DAB1 Complex in State A -

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Basic information

Entry
Database: PDB / ID: 38rh
TitleStructure of the DAB1 Complex in State A
Components
  • NADH/Ubiquinone/plastoquinone (Complex I)
  • Probable inorganic carbon transporter subunit DabA
KeywordsLYASE / transmembrane protein / carbonic anhydrase / CO2-concentrating mechanism / CO2 transporter
Function / homology
Function and homology information


electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Probable inorganic carbon transporter subunit DabA / 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 DabA / NADH/Ubiquinone/plastoquinone (Complex I)
Similarity search - Component
Biological speciesThermocrinis albus DSM 14484 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsPhillips, N.R. / Oltrogge, L.M. / Remis, J.P. / Savage, D.F.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0016240 (DFS) United States
CitationJournal: To Be Published
Title: Structural insights into the coupling mechanism of vectorial CO2 uptake by DAB1
Authors: Phillips, N.R. / Oltrogge, L.M. / Remis, J.P. / Savage, D.F.
History
DepositionSep 15, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / 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 DabA
B: NADH/Ubiquinone/plastoquinone (Complex I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,3623
Polymers207,2962
Non-polymers651
Water11,638646
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Probable inorganic carbon transporter subunit DabA


Mass: 119379.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermocrinis albus DSM 14484 (bacteria)
Strain: DSM 14484 / JCM 11386 / HI 11/12 / Gene: dabA, Thal_0253 / Production host: Escherichia coli (E. coli) / References: UniProt: D3SP01
#2: Protein NADH/Ubiquinone/plastoquinone (Complex I)


Mass: 87917.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermocrinis albus DSM 14484 (bacteria)
Strain: DSM 14484 / JCM 11386 / HI 11/12 / Gene: Thal_0254 / Production host: Escherichia coli (E. coli) / References: UniProt: D3SP02
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: DAB1 complex with Zn cofactor in detergent micelle / Type: COMPLEX / Entity ID: #2, #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Thermocrinis albus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21-AI
Buffer solutionpH: 7.5
Details: 50 mM HEPES, 300 mM NaCl, 10 micromolar ZnCl2, 0.001% w/v LMNG
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESC8H18N2O4S1
2300 mMsodium chlorideNaCl1
310 micromolarzinc chlorideZnCl21
40.001 percentLauryl Maltose Neopentyl GlycolC47H88O221
SpecimenConc.: 0.09 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was purified via Ni-IMAC, heat treatment, and SEC. Aliquots of the elution peak on SEC were flash frozen and stored at -80 until imaging.
Specimen supportDetails: Deposited graphene oxide on the grid prior to use / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K / Details: 3s blot time, blot force 3

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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: 1800 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.0particle selection
2SerialEM4.2.19image acquisition
4cryoSPARC4.7.0CTF correction
7PHENIXdev-6003model fitting
9PHENIXdev-6003model refinement
12cryoSPARC4.7.0classification
13cryoSPARC4.7.03D reconstruction
CTF correctionDetails: Patch CTF used in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164827 / Details: cryoSPARC non-uniform refinement / Symmetry type: POINT

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