6S3K | pdb_00006s3k

KimA from Bacillus subtilis in inward-facing, occluded state

• PDB DOI: https://doi.org/10.2210/pdb6S3K/pdb
• EM Map EMD-10092: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2019-06-25 Released: 2020-02-12 
• Deposition Author(s): Tascon, I., Sousa, J.S., Vonck, J., Haenelt, I.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of proton-coupled potassium transport in the KUP family.

Tascon, I., Sousa, J.S., Corey, R.A., Mills, D.J., Griwatz, D., Aumuller, N., Mikusevic, V., Stansfeld, P.J., Vonck, J., Hanelt, I.

(2020) Nat Commun 11: 626-626

• PubMed: 32005818 
• DOI: https://doi.org/10.1038/s41467-020-14441-7
• Primary Citation Related Structures: 
  6S3K


• PubMed 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 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.

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Organizational Affiliation: 
• Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
Department of Biochemistry, University of Oxford, Oxford, UK.
School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany. [e-mail].
Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 133.91 kDa 
• Atom Count: 8,902 
• Modeled Residue Count: 1,146 
• Deposited Residue Count: 1,214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APC family permease	A [auth B], B [auth A]	607	Bacillus subtilis	Mutation(s): 0  Gene Names: B4417_2855, ETK71_02405 Membrane Entity: Yes
UniProt
Find proteins for P96589 (Bacillus subtilis (strain 168)) Explore P96589  Go to UniProtKB:  P96589

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	C [auth B], D [auth B], E [auth B], F [auth A], G [auth A], H [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-12 
Deposition Author(s): Tascon, I., Sousa, J.S., Vonck, J., Haenelt, I.

Revision History  

• Version 1.0: 2020-02-12
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection, Database references
• Version 1.2: 2025-07-02
  Changes: Data collection, Structure summary