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- EMDB-79079: Structure of the DAB1 Complex in State A -

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Basic information

Entry
Database: EMDB / ID: EMD-79079
TitleStructure of the DAB1 Complex in State A
Map dataCropped, density modified, and sharpened map of State A used for model building and interpretation.
Sample
  • Complex: DAB1 complex with Zn cofactor in detergent micelle
    • Protein or peptide: NADH/Ubiquinone/plastoquinone (Complex I)
    • Protein or peptide: Probable inorganic carbon transporter subunit DabA
  • Ligand: ZINC ION
  • Ligand: water
Keywordstransmembrane protein / carbonic anhydrase / CO2-concentrating mechanism / CO2 transporter / LYASE
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 (bacteria) / Thermocrinis albus DSM 14484 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsPhillips NR / Oltrogge LM / Remis JP / Savage DF
Funding support United States, 1 items
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 NR / Oltrogge LM / Remis JP / Savage DF
History
DepositionSep 15, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_79079.png

Downloads & links

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Map

FileDownload / File: emd_79079.map.gz / Format: CCP4 / Size: 37.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCropped, density modified, and sharpened map of State A used for model building and interpretation.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.53 Å/pix.
x 172 pix.
= 90.3 Å		0.53 Å/pix.
x 226 pix.
= 118.65 Å		0.53 Å/pix.
x 255 pix.
= 133.875 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.525 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.205
Minimum - Maximum-2.608682 - 4.6714363
Average (Standard dev.)-0.000000000002138 (±0.32344928)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin161154218
Dimensions226255172
Spacing172226255
CellA: 90.299995 Å / B: 118.649994 Å / C: 133.875 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map from final non-uniform refinement of State A

Fileemd_79079_half_map_1.map
AnnotationHalf map from final non-uniform refinement of State A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map from final non-uniform refinement of State A

Fileemd_79079_half_map_2.map
AnnotationHalf map from final non-uniform refinement of State A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DAB1 complex with Zn cofactor in detergent micelle

EntireName: DAB1 complex with Zn cofactor in detergent micelle
Components
  • Complex: DAB1 complex with Zn cofactor in detergent micelle
    • Protein or peptide: NADH/Ubiquinone/plastoquinone (Complex I)
    • Protein or peptide: Probable inorganic carbon transporter subunit DabA
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: DAB1 complex with Zn cofactor in detergent micelle

SupramoleculeName: DAB1 complex with Zn cofactor in detergent micelle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Thermocrinis albus (bacteria)

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Macromolecule #1: Probable inorganic carbon transporter subunit DabA

MacromoleculeName: Probable inorganic carbon transporter subunit DabA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermocrinis albus DSM 14484 (bacteria) / Strain: DSM 14484 / JCM 11386 / HI 11/12
Molecular weightTheoretical: 119.379078 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEKGRKLYIR SLVNMAAEPI AYFWPMRTFI TRNPLRGLED KPFKDALKEG ELLFGGRGYL RREDYRYLYS KGYMKDEFLR EGIRKFLSS MELKLELPYE ELLFTLFVDN IKEPALNDLY KGKVDEKILN ALMEHFTEDP AQVCRDILLS IGLKHTLQDI I ELLTGKNL ...String:
MEKGRKLYIR SLVNMAAEPI AYFWPMRTFI TRNPLRGLED KPFKDALKEG ELLFGGRGYL RREDYRYLYS KGYMKDEFLR EGIRKFLSS MELKLELPYE ELLFTLFVDN IKEPALNDLY KGKVDEKILN ALMEHFTEDP AQVCRDILLS IGLKHTLQDI I ELLTGKNL SQTIDELTIK TAFDFLDEGQ STIDMPGRGA GFYKAWRELA KRNLRFFLWA GKSLKDMVEA FQEPEPAIEY VL TSFELPQ ALWEGYISLE LARLKGIAGF IKWRSHNKFY YWQKVHPVDM VDYTAIRLLI AKAVIDAHKK GLPFEPTYRA LEE FLNKER ARAYLLYELG TKRCPPQLWD RMKDYLKKPH EKVEEYVRAK AEILALSYYL FLTNWTRKVG IDINSLTADH LLEL MKVYE KFKEEEGYIY LRALEDTHID KLVKLIRAPQ EETQERPLAQ AFFCIDVRSE RFRRHLESLG RYQTYGIAGF FGVPV AMVN LQKGHEEFLC PVIVTPRNVV FEVPYNKRGV EKERVASHIF HSVKDHVLAP FVAVEMLGFA FGFDFLGKTF LPEKYL RFK DLAFKDYTKT SLIVNKLSDE EIQQIIQSYY STLIRTVLRE RFGMQTINDE MVNQVYEACL NGGNTLSENL KEVVELL RE KYKVERGYVE LFRERLKSVG FTKEEQAFLI STALKSIGLT KEFAPIVLVL GHESRSENNP YESALDCGAC GGASGIYN A RIFCIMANDH VVRQIMAQRY GLEIPPYTVF IPGVHNTTTD EVFLYDLEFL PAEYIPLIDK IIQDLQVAKD LTLQERAKT LDTKNTQDVY KKAYDWSEVR PEWGLSGNYA FIIGRRSITK LANLDGRVFL HSYDYRVDKK GFLLENILAG PAVVGQWINS EYYFSTVDN EVYGSGSKVY HNVVGRIGVM TGNYSDLRTG LPAQTVLKEG KPFHIPIRYT LIVEAPFELA RNAINKIRKI R DLMQNGWI NLLIFDPEKE IFYRYLEGVW VEYFKKEEVK AGGSGWSHPQ FEKGGGSGGG SGGSAWSHPQ FEK

UniProtKB: Probable inorganic carbon transporter subunit DabA

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Macromolecule #2: NADH/Ubiquinone/plastoquinone (Complex I)

MacromoleculeName: NADH/Ubiquinone/plastoquinone (Complex I) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermocrinis albus DSM 14484 (bacteria) / Strain: DSM 14484 / JCM 11386 / HI 11/12
Molecular weightTheoretical: 87.917086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFPEVAIVII PLLSMITSLF TEKRTYAKVS TLFTGMAFLL SLYVLIFTNK ESSLLFLRFD GLGTLLASYI LLVSTVIHKY SENYMKDEQ GFKRYFLLLD LMTWNLLLLV LSNHLIILFA SWHLMGVILY FLLTFNNRRE QAVQSGRTAL FTHRIADVPL L VAILLLYQ ...String:
MFPEVAIVII PLLSMITSLF TEKRTYAKVS TLFTGMAFLL SLYVLIFTNK ESSLLFLRFD GLGTLLASYI LLVSTVIHKY SENYMKDEQ GFKRYFLLLD LMTWNLLLLV LSNHLIILFA SWHLMGVILY FLLTFNNRRE QAVQSGRTAL FTHRIADVPL L VAILLLYQ QYGTFEISKL AQMITTGPSD TLWIVTLLVI LSGIIKSAQI PFHVWLVYSM EGPTPVSALM HAGIVNAGAF IA NRFAFMF PHDLYGLSLS FLIGLITAIV GSTLMLMQND VKKALGYSTV GQMGYMMMEI GVGAFALALY HMMAHGIFKA TLF LSSGGV IHEARRDTNI PRDEVYDALV KREMSFKEIP TVFYGAVTLI VPFVLVLVTH LFFEQDVFRY KAPLILLFFG WVTS AQILF NLFKMGKEKP LLTIFLGGFS LFLLLSVYTF MSHILQVFVF TYEGLQEEIY RRAFSNAPLF FLSMILSLIL VLAGW VLIY FANEEKPLKL HLSLYAHLSR ELYFPDLYKL TGKLFLRLAR VLSITSSSVV PVYGFFYQGG SSGSFLLKVF LLSLFI PLF PISLITSYLI KRFWIYSYPT IALLGFITLK LTHLPAYEPL HYLAALTLIF HSVRATLSEN FKESVSELYP ALLSITW IS GDDHFVLLLL PSLLLYLLGV YIKKVLQTDS FYYAGGLMEK MPIYSLLLVI VSLQACLTPV MPSFYSFFEA LLRSNTLQ I ILLVMGWFTL GVAVALSVWR LLHGKPRDDI RYADILRRSG SSAHHHHHHH HH

UniProtKB: NADH/Ubiquinone/plastoquinone (Complex I)

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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: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 646 / 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

Concentration0.09 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
300.0 mMNaClsodium chloride
10.0 micromolarZnCl2zinc chloride
0.001 percentC47H88O22Lauryl Maltose Neopentyl Glycol

Details: 50 mM HEPES, 300 mM NaCl, 10 micromolar ZnCl2, 0.001% w/v LMNG
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 / Details: Deposited graphene oxide on the grid prior to use
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV / Details: 3s blot time, blot force 3.
DetailsSample 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.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Details: Patch CTF used in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio model was generated in cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Details: cryoSPARC non-uniform refinement / Number images used: 164827
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 6 / Avg.num./class: 151463 / Software - Name: cryoSPARC (ver. 4.7.0)
Details: The two most populated classes were used to obtain maps of State A and B. This map corresponds to State A with 164,827 particles.
FSC plot (resolution estimation)

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