6CPV | pdb_00006cpv

MicroED structure of NaK ion channel reveals a process of Na+ partition into the selectivity filter

• PDB DOI: https://doi.org/10.2210/pdb6CPV/pdb
• EM Map EMD-7558: EMDB EMDataResource

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


• Deposited: 2018-03-14 Released: 2018-09-12 
• Deposition Author(s): Liu, S., Gonen, T.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.50 Å
• R-Value Free: 
  0.263 (Depositor) 
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

MicroED structure of the NaK ion channel reveals a Na+partition process into the selectivity filter.

Liu, S., Gonen, T.

(2018) Commun Biol 1: 38-38

• PubMed: 30167468 
• DOI: https://doi.org/10.1038/s42003-018-0040-8
• Primary Citation Related Structures: 
  6CPV


• PubMed Abstract: 
  

  Sodium (Na ⁺ ) is a ubiquitous and important inorganic salt mediating many critical biological processes such as neuronal excitation, signaling, and facilitation of various transporters. The hydration states of Na ⁺ are proposed to play critical roles in determining the conductance and the selectivity of Na ⁺ channels, yet they are rarely captured by conventional structural biology means. Here we use the emerging cryo-electron microscopy (cryoEM) method micro-electron diffraction (MicroED) to study the structure of a prototypical tetrameric Na ⁺ -conducting channel, NaK, to 2.5 Å resolution from nano-crystals. Two new conformations at the external site of NaK are identified, allowing us to visualize a partially hydrated Na ⁺ ion at the entrance of the channel pore. A process of dilation coupled with Na ⁺ movement is identified leading to valuable insights into the mechanism of ion conduction and gating. This study lays the ground work for future studies using MicroED in membrane protein biophysics.

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Organizational Affiliation: 
• Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA.
Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA. [e-mail].
Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA. [e-mail].
Departments of Physiology and Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA. [e-mail].

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 Evidence: gel filtration

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: 21.81 kDa 
• Atom Count: 1,494 
• Modeled Residue Count: 187 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium channel protein	A, B	96	Bacillus cereus	Mutation(s): 0  Gene Names: A9485_19160, B4155_3291, BACERE00184_02078, CN419_22740, CN950_06075, CN980_22870, COI98_17615, COK18_26145, 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	K [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
NA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.50 Å
• R-Value Free:  0.263 (Depositor) 
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.072	α = 90
b = 68.072	β = 90
c = 89.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Liu, S., Gonen, T.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	1

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description