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Yorodumi- EMDB-24683: Cryo-EM Structure of the Sodium-driven Chloride/Bicarbonate Excha... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24683 | |||||||||
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Title | Cryo-EM Structure of the Sodium-driven Chloride/Bicarbonate Exchanger NDCBE (SLC4A8) | |||||||||
Map data | postprocess 3d map. | |||||||||
Sample |
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Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Wang WG / Tsirulnikov K / Zhekova H / Kayik G / Muhammad-Khan H / Azimov R / Abuladze N / Kao L / Newman D / Noskov SY ...Wang WG / Tsirulnikov K / Zhekova H / Kayik G / Muhammad-Khan H / Azimov R / Abuladze N / Kao L / Newman D / Noskov SY / Zhou ZH / Pushkin A / Kurtz I | |||||||||
Funding support | United States, Canada, 2 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Cryo-EM structure of the sodium-driven chloride/bicarbonate exchanger NDCBE. Authors: Weiguang Wang / Kirill Tsirulnikov / Hristina R Zhekova / Gülru Kayık / Hanif Muhammad Khan / Rustam Azimov / Natalia Abuladze / Liyo Kao / Debbie Newman / Sergei Yu Noskov / Z Hong Zhou / ...Authors: Weiguang Wang / Kirill Tsirulnikov / Hristina R Zhekova / Gülru Kayık / Hanif Muhammad Khan / Rustam Azimov / Natalia Abuladze / Liyo Kao / Debbie Newman / Sergei Yu Noskov / Z Hong Zhou / Alexander Pushkin / Ira Kurtz / Abstract: SLC4 transporters play significant roles in pH regulation and cellular sodium transport. The previously solved structures of the outward facing (OF) conformation for AE1 (SLC4A1) and NBCe1 (SLC4A4) ...SLC4 transporters play significant roles in pH regulation and cellular sodium transport. The previously solved structures of the outward facing (OF) conformation for AE1 (SLC4A1) and NBCe1 (SLC4A4) transporters revealed an identical overall fold despite their different transport modes (chloride/bicarbonate exchange versus sodium-carbonate cotransport). However, the exact mechanism determining the different transport modes in the SLC4 family remains unknown. In this work, we report the cryo-EM 3.4 Å structure of the OF conformation of NDCBE (SLC4A8), which shares transport properties with both AE1 and NBCe1 by mediating the electroneutral exchange of sodium-carbonate with chloride. This structure features a fully resolved extracellular loop 3 and well-defined densities corresponding to sodium and carbonate ions in the tentative substrate binding pocket. Further, we combine computational modeling with functional studies to unravel the molecular determinants involved in NDCBE and SLC4 transport. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24683.map.gz | 54.5 MB | EMDB map data format | |
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Header (meta data) | emd-24683-v30.xml emd-24683.xml | 22.4 KB 22.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24683_fsc.xml | 8.8 KB | Display | FSC data file |
Images | emd_24683.png | 104.4 KB | ||
Others | emd_24683_additional_1.map.gz emd_24683_half_map_1.map.gz emd_24683_half_map_2.map.gz | 54.5 MB 43.9 MB 43.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24683 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24683 | HTTPS FTP |
-Validation report
Summary document | emd_24683_validation.pdf.gz | 678.4 KB | Display | EMDB validaton report |
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Full document | emd_24683_full_validation.pdf.gz | 677.9 KB | Display | |
Data in XML | emd_24683_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | emd_24683_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24683 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24683 | HTTPS FTP |
-Related structure data
Related structure data | 7rtmMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_24683.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | postprocess 3d map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: postprocess 3d map.
File | emd_24683_additional_1.map | ||||||||||||
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Annotation | postprocess 3d map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map1.
File | emd_24683_half_map_1.map | ||||||||||||
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Annotation | half map1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map2.
File | emd_24683_half_map_2.map | ||||||||||||
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Annotation | half map2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NDCBE(SLC4A8) dimer
Entire | Name: NDCBE(SLC4A8) dimer |
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Components |
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-Supramolecule #1: NDCBE(SLC4A8) dimer
Supramolecule | Name: NDCBE(SLC4A8) dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Electroneutral sodium bicarbonate exchanger 1
Macromolecule | Name: Electroneutral sodium bicarbonate exchanger 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 64.304094 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LFGGLVLDVK RKAPWYWSDY RDALSLQCLA SFLFLYCACM SPVITFGGLL GEATEGRISA IESLFGASMT GIAYSLFAGQ PLTILGSTG PVLVFEKILF KFCKDYALSY LSLRACIGLW TAFLCIVLVA TDASSLVCYI TRFTEEAFAS LICIIFIYEA I EKLIHLAE ...String: LFGGLVLDVK RKAPWYWSDY RDALSLQCLA SFLFLYCACM SPVITFGGLL GEATEGRISA IESLFGASMT GIAYSLFAGQ PLTILGSTG PVLVFEKILF KFCKDYALSY LSLRACIGLW TAFLCIVLVA TDASSLVCYI TRFTEEAFAS LICIIFIYEA I EKLIHLAE TYPIHMHSQL DHLSLYYCRC ALPENPNNHT LQYWKEHSIP TADVNWANLT VSECQEMHGE FIGSACGHHG PY TPDVLFW SCILFFATFI VSSTLKTFKT SRYFPTRVRS TVSDFAVFLT IFTMVILDFL IGVPSPKLQV PSVFKPTRDD RGW FISPIG PNPWWTVIAA IIPALLCTIL IFMDQQITAV IINRKEHKLK KGCGYHLDLL VVAIMLGVCS LMGLPWFVAA TVLS ITHVN SLKLESECSA PGEQPKFLGI REQRVTGLMI FVLMGCSVFM TAVLKFIPMP VLYGVFLYMG VSSLQGIQFF DRLKL FGMP AKHQPDFIYL RHVPLRKVHL FTLVQLTCLV LLWVIKASPA AIVFPMMVLA LVFVRKVMDL CFSKRELSWL DDLMPE SKK KKLDDAKK |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #4: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 4 / Number of copies: 2 |
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Molecular weight | Theoretical: 22.99 Da |
-Macromolecule #5: CARBONATE ION
Macromolecule | Name: CARBONATE ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: CO3 |
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Molecular weight | Theoretical: 60.009 Da |
Chemical component information | ChemComp-CO3: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Details: Glow discharged with Easyglow. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 2 seconds. blot force 0. | ||||||||||||
Details | sample in 0.01% LMNG. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 2 / Number real images: 7545 / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Target criteria: Correlation coefficient |
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Output model | PDB-7rtm: |