6S5C | pdb_00006s5c

Square conformation of KtrA WT ring with bound ATP and calcium

• PDB DOI: https://doi.org/10.2210/pdb6S5C/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-01 Released: 2020-01-08 
• Deposition Author(s): Teixeira-Duarte, C.M., Fonseca, F., Morais-Cabral, J.H.
• Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.259 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Activation of a nucleotide-dependent RCK domain requires binding of a cation cofactor to a conserved site.

Teixeira-Duarte, C.M., Fonseca, F., Morais Cabral, J.H.

(2019) Elife 8

• PubMed: 31868587 
• DOI: https://doi.org/10.7554/eLife.50661
• Primary Citation Related Structures: 
  6S2J, 6S5B, 6S5C, 6S5D, 6S5E, 6S5G, 6S5N, 6S5O, 6S7R


• PubMed Abstract: 
  

  RCK domains regulate the activity of K ⁺ channels and transporters in eukaryotic and prokaryotic organisms by responding to ions or nucleotides. The mechanisms of RCK activation by Ca ²⁺ in the eukaryotic BK and bacterial MthK K ⁺ channels are well understood. However, the molecular details of activation in nucleotide-dependent RCK domains are not clear. Through a functional and structural analysis of the mechanism of ATP activation in KtrA, a RCK domain from the B. subtilis KtrAB cation channel, we have found that activation by nucleotide requires binding of cations to an intra-dimer interface site in the RCK dimer. In particular, divalent cations are coordinated by the γ-phosphates of bound-ATP, tethering the two subunits and stabilizing the active state conformation. Strikingly, the binding site residues are highly conserved in many different nucleotide-dependent RCK domains, indicating that divalent cations are a general cofactor in the regulatory mechanism of many nucleotide-dependent RCK domains.

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Organizational Affiliation: 
• Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.
Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.
Programa Doutoral em Biologia Molecular e Celular (MCbiology), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.89 kDa 
• Atom Count: 3,475 
• Modeled Residue Count: 434 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ktr system potassium uptake protein A	A, B	222	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: ktrA, yuaA, BSU31090
UniProt
Find proteins for O32080 (Bacillus subtilis (strain 168)) Explore O32080  Go to UniProtKB:  O32080

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	C [auth A], E [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA (Subject of Investigation/LOI)	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.259 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.693	α = 90
b = 122.693	β = 90
c = 84.012	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-01-08 
Deposition Author(s): Teixeira-Duarte, C.M., Fonseca, F., Morais-Cabral, J.H.

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Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BIA-BQM/29863/2017
Fundacao para a Ciencia e a Tecnologia	Portugal	POCI-01-0145-FEDER-007274

Revision History  

• Version 1.0: 2020-01-08
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description