+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10092 | |||||||||
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Title | KimA from Bacillus subtilis in inward-facing, occluded state | |||||||||
Map data | None | |||||||||
Sample |
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Keywords | potassium transporter / LeuT fold / symporter / SMALP / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information symporter activity / transmembrane transporter activity / potassium ion transport / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Tascon I / Sousa JS | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis of proton-coupled potassium transport in the KUP family. Authors: Igor Tascón / Joana S Sousa / Robin A Corey / Deryck J Mills / David Griwatz / Nadine Aumüller / Vedrana Mikusevic / Phillip J Stansfeld / Janet Vonck / Inga Hänelt / Abstract: Potassium homeostasis is vital for all organisms, but is challenging in single-celled organisms like bacteria and yeast and immobile organisms like plants that constantly need to adapt to changing ...Potassium homeostasis is vital for all organisms, but is challenging in single-celled organisms like bacteria and yeast and immobile organisms like plants that constantly need to adapt to changing external conditions. KUP transporters facilitate potassium uptake by the co-transport of protons. Here, we uncover the molecular basis for transport in this widely distributed family. We identify the potassium importer KimA from Bacillus subtilis as a member of the KUP family, demonstrate that it functions as a K/H symporter and report a 3.7 Å cryo-EM structure of the KimA homodimer in an inward-occluded, trans-inhibited conformation. By introducing point mutations, we identify key residues for potassium and proton binding, which are conserved among other KUP proteins. | |||||||||
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_10092.map.gz | 26.5 MB | EMDB map data format | |
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Header (meta data) | emd-10092-v30.xml emd-10092.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_10092.png | 181.4 KB | ||
Filedesc metadata | emd-10092.cif.gz | 5.4 KB | ||
Others | emd_10092_half_map_1.map.gz emd_10092_half_map_2.map.gz | 31.8 MB 31.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10092 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10092 | HTTPS FTP |
-Validation report
Summary document | emd_10092_validation.pdf.gz | 469.4 KB | Display | EMDB validaton report |
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Full document | emd_10092_full_validation.pdf.gz | 468.5 KB | Display | |
Data in XML | emd_10092_validation.xml.gz | 9.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10092 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10092 | HTTPS FTP |
-Related structure data
Related structure data | 6s3kMC 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_10092.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.077 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: KimA half-map1
File | emd_10092_half_map_1.map | ||||||||||||
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Annotation | KimA half-map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: KimA half-map2
File | emd_10092_half_map_2.map | ||||||||||||
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Annotation | KimA half-map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : KimA
Entire | Name: KimA |
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Components |
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-Supramolecule #1: KimA
Supramolecule | Name: KimA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
-Macromolecule #1: APC family permease
Macromolecule | Name: APC family permease / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 66.838977 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MYHSIKRFLI GKPLKSQAAG EQKLTKLKAL AMLSSDALSS VAYGTEQILI ILATISAAAF WYSIPIAVGV LILLLALILS YRQIIYAYP QGGGAYIVSK ENLGEKPGLI AGGSLLVDYI LTVAVSISAG TDAITSAFPA LHDYHVPIAI FLVLVIMILN L RGLSESAS ...String: MYHSIKRFLI GKPLKSQAAG EQKLTKLKAL AMLSSDALSS VAYGTEQILI ILATISAAAF WYSIPIAVGV LILLLALILS YRQIIYAYP QGGGAYIVSK ENLGEKPGLI AGGSLLVDYI LTVAVSISAG TDAITSAFPA LHDYHVPIAI FLVLVIMILN L RGLSESAS ILAYPVYLFV VALLVLIAVG LFKLMTGQID QPAHHTSLGT PVAGITLFLL LKAFSSGCSA LTGVEAISNA IP AFKNPPA RNAARTLAMM GILLAILFSG ITVLAYGYGT APKPDETVVS QIASETFGRN VFYYVIQGVT SLILVLAANT GFS AFPQLA FNLARDQYMP RMFTVRGDRL GFSNGIIFLG FASIVLIILF GGQTEHLIPL YAVGVFIPFT LSQTGMCMKW IKQK PKGWI GKMLINSCGA LISFMVLSIL FVTKFNVVWP VLIFMPIVVL LFFAIKNHYT AVGEQLRIVD KEPEEIKGTV VIVPV AGVT TVVQKSIHYA KSLSDQVIAV HVSFDREQEK KFEKRWEELN NGVRLVTLHS SYRSLVHPFD KFLETVEAKA KKEQFS VMV LFPQFITKKR WHTILHNQSA FLLRVRLFWK KDIMVATLPY HFKK UniProtKB: Amino acid permease |
-Macromolecule #2: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.77 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 149724 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |