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- EMDB-63973: Cryo-EM structure of cyanobacterial bicarbonate transporter CmpBCD -

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Basic information

Entry
Database: EMDB / ID: EMD-63973
TitleCryo-EM structure of cyanobacterial bicarbonate transporter CmpBCD
Map data
Sample
  • Complex: Bicarbonate importer CmpBCD.
    • Protein or peptide: CmpB
    • Protein or peptide: CmpC
    • Protein or peptide: CmpD
KeywordsABC transporter / bicarbonate importer / membrane transporter / nitrate binding / MEMBRANE PROTEIN
Biological speciesPseudanabaena sp. Chao 1811 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi QY / Li B / Zhou CZ / Jiang YL
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of cyanobacterial bicarbonate transporter CmpBCD
Authors: Li QY / Li B / Zhou CZ / Jiang YL
History
DepositionMar 30, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63973.png

Downloads & links

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Map

FileDownload / File: emd_63973.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-0.90899944 - 1.5136893
Average (Standard dev.)-0.00000029543992 (±0.036000766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63973_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63973_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 : Bicarbonate importer CmpBCD.

EntireName: Bicarbonate importer CmpBCD.
Components
  • Complex: Bicarbonate importer CmpBCD.
    • Protein or peptide: CmpB
    • Protein or peptide: CmpC
    • Protein or peptide: CmpD

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Supramolecule #1: Bicarbonate importer CmpBCD.

SupramoleculeName: Bicarbonate importer CmpBCD. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudanabaena sp. Chao 1811 (bacteria)

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Macromolecule #1: CmpB

MacromoleculeName: CmpB / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudanabaena sp. Chao 1811 (bacteria)
Molecular weightTheoretical: 30.966502 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAASIGNRNG SFGRSLSKFW EKNAQNWALP IVGILGFLIV WQLLTWTGLL KLPGPWDIMA EKSTRNLLLY PFFDRGGTDK GLFWQTLAS FERVAKGYSI AAIVGISVGI LVGTNAVIDK ALDPLFQFLR TVPPLAWVPI ALAALRQNEP AALFVIFITA V WPILLNTA ...String:
MAASIGNRNG SFGRSLSKFW EKNAQNWALP IVGILGFLIV WQLLTWTGLL KLPGPWDIMA EKSTRNLLLY PFFDRGGTDK GLFWQTLAS FERVAKGYSI AAIVGISVGI LVGTNAVIDK ALDPLFQFLR TVPPLAWVPI ALAALRQNEP AALFVIFITA V WPILLNTA VGVKQIPQDY RNVSRVLQLS KQKYFFKILI PSALPYIFTG LRISIGLAWL AIIAAEIIMS GIVGIGFFIW NS YTNDKVG EVILALVYIG AVGLILDRAV AWLQNVILPE EQK

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Macromolecule #2: CmpC

MacromoleculeName: CmpC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudanabaena sp. Chao 1811 (bacteria)
Molecular weightTheoretical: 73.984109 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQDFVLVDQV ERTFPLGGGK EYIALKGIDL QIRKGEFISL IGHSGCGKST LLNMIAGLDL PSGGVVMLED ERVTRPGPDR MVVFQNYSL LPWLSVRENV ALAVDEVLSH LPKGERHDLV ERYVNMVGLA HAIDKPPTQL SGGMRQRVAI ARALAVRPKL L LLDEPFGA ...String:
MQDFVLVDQV ERTFPLGGGK EYIALKGIDL QIRKGEFISL IGHSGCGKST LLNMIAGLDL PSGGVVMLED ERVTRPGPDR MVVFQNYSL LPWLSVRENV ALAVDEVLSH LPKGERHDLV ERYVNMVGLA HAIDKPPTQL SGGMRQRVAI ARALAVRPKL L LLDEPFGA LDALTRGNLQ EKLMQICNED QITAVMVTHD VDEAVLLSDR IVMLTNGPAS KIGNILEVDI PRPRQRMEAV NH PSYYSLR SEIIYFLNQQ KRVKKLNARK VTTVAKHGLE KVNLEIGFVP LTACAPIAVA KEKGFFEKHG LDEVSLVRET SWR GIVDGI SGGYLDAAQM PSGLPMWLTL GGAGACKPIV TALTMTRNGN AITLDKHFYD RGIHTLADFK AMLQSTRDRQ HRMG VVHPS SMHNLLLRYW LAAGGIDPDL DVELKTIPPA QMVVDLKAGS IDGFCVGEPW NFRAAMENIG FTVATDLEIW NGHPG KVLG VREDWANAYP NTHIALVKAL LEACMYCADP NNAEEIRQIL SRRAYVSTNV NYIHLGNPDD VTCALDTPMR EPAHHQ FYG AGVNRPSRSE HLWHITQMAR WGDVPFPRNW VEVLEKTCRV GVFSTAAREL GLTDITYSRN AIQLFDDIPF NAEDPIG YL NHLDIKRNIT MAEIAMESVR MVA

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Macromolecule #3: CmpD

MacromoleculeName: CmpD / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudanabaena sp. Chao 1811 (bacteria)
Molecular weightTheoretical: 31.282113 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTQTILEHTN QIAQIPPQES FLRIENVSKI YPTPKGEYVV LKDVNLHIQE GEFICLIGHS GCGKSTLLNM VGGFSKPSIG EVTVNGKLI TKPGPDRMVV FQGYALLPWL TVYENVMLAV DSVNPNLSKS EKNDIVRHHL AMVGLSEAAE KKPTQISGGM K QRVSIARA ...String:
MTQTILEHTN QIAQIPPQES FLRIENVSKI YPTPKGEYVV LKDVNLHIQE GEFICLIGHS GCGKSTLLNM VGGFSKPSIG EVTVNGKLI TKPGPDRMVV FQGYALLPWL TVYENVMLAV DSVNPNLSKS EKNDIVRHHL AMVGLSEAAE KKPTQISGGM K QRVSIARA LAIRPEVLIL DEPFGALDAI TKEELQEELL QIWTEHRCTV LMITHDIDEA LFLADRLVMM TNGPAANIGE IM RIPFPRP RDRAQIMEDP LYYDLRNTAL DFLYNRFAHD E

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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

Concentration5.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.5 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 210668
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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