6UFE | pdb_00006ufe

The structure of a potassium selective ion channel at atomic resolution

• PDB DOI: https://doi.org/10.2210/pdb6UFE/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Bacillus cereus
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2019-09-24 Released: 2020-08-05 
• Deposition Author(s): Langan, P.S., Vandavasi, V.G., Sullivan, B., Afonine, P.V., Weiss, K.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.148 (Depositor), 0.147 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.133 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation.

Langan, P.S., Vandavasi, V.G., Kopec, W., Sullivan, B., Afonne, P.V., Weiss, K.L., de Groot, B.L., Coates, L.

(2020) IUCrJ 7: 835-843

• PubMed: 32939275 
• DOI: https://doi.org/10.1107/S2052252520008271
• Primary Citation Related Structures: 
  6UFE


• PubMed Abstract: 
  

  Protein dynamics are essential to function. One example of this is the various gating mechanisms within ion channels, which are transmembrane proteins that act as gateways into the cell. Typical ion channels switch between an open and closed state via a conformational transition which is often triggered by an external stimulus, such as ligand binding or pH and voltage differences. The atomic resolution structure of a potassium-selective ion channel named NaK2K has allowed us to observe that a hydro-phobic residue at the bottom of the selectivity filter, Phe92, appears in dual conformations. One of the two conformations of Phe92 restricts the diameter of the exit pore around the selectivity filter, limiting ion flow through the channel, while the other conformation of Phe92 provides a larger-diameter exit pore from the selectivity filter. Thus, it can be concluded that Phe92 acts as a hydro-phobic gate, regulating the flow of ions through the selectivity filter.

---

Organizational Affiliation: 
• Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA.
Lentigen Technologies, 910 Clopper Road, Gaithersburg, MD 20878, USA.
Department of Chemistry, Princeton University, Princeton, NJ 08540, USA.
Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.89 kDa 
• Atom Count: 1,708 
• Modeled Residue Count: 182 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transporter	A, B	92	Bacillus cereus	Mutation(s): 2  Gene Names: A9485_19160, BACERE00184_02078, CJ306_03585, CN950_06075, CN980_22870, COI98_17615, CON37_12595 Membrane Entity: Yes
UniProt
Find proteins for Q81HW2 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81HW2  Go to UniProtKB:  Q81HW2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth A], E [auth A], F [auth A], K [auth B], L [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
K	G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.148 (Depositor), 0.147 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.133 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.86	α = 90
b = 67.86	β = 90
c = 89.62	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Langan, P.S., Vandavasi, V.G., Sullivan, B., Afonine, P.V., Weiss, K.L.

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2020-09-30
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description