+Open data
-Basic information
Entry | Database: PDB / ID: 6s3k | ||||||
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Title | KimA from Bacillus subtilis in inward-facing, occluded state | ||||||
Components | APC family permease | ||||||
Keywords | TRANSPORT PROTEIN / potassium transporter / LeuT fold / symporter / SMALP | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Tascon, I. / Sousa, J.S. / Vonck, J. / Haenelt, I. | ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6s3k.cif.gz | 201.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s3k.ent.gz | 162.7 KB | Display | PDB format |
PDBx/mmJSON format | 6s3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s3k_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6s3k_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6s3k_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 6s3k_validation.cif.gz | 58.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/6s3k ftp://data.pdbj.org/pub/pdb/validation_reports/s3/6s3k | HTTPS FTP |
-Related structure data
Related structure data | 10092MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 66838.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_2855, ETK71_02405 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A164U4X9, UniProt: P96589*PLUS #2: Chemical | ChemComp-K / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: KimA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.77 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | |||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149724 / Symmetry type: POINT |