4H37

Crystal structure of a voltage-gated K+ channel pore domain in a closed state in lipid membranes

• PDB DOI: https://doi.org/10.2210/pdb4H37/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2012-09-13 Released: 2012-11-07 
• Deposition Author(s): Santos, J.S., Asmar-Rovira, G.A., Han, G.W., Liu, W., Syeda, R., Cherezov, V., Baker, K.A., Stevens, R.C., Montal, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 0.341 
• R-Value Work: 0.314 
• R-Value Observed: 0.318 

Literature

Crystal Structure of a Voltage-gated K+ Channel Pore Module in a Closed State in Lipid Membranes.

Santos, J.S., Asmar-Rovira, G.A., Han, G.W., Liu, W., Syeda, R., Cherezov, V., Baker, K.A., Stevens, R.C., Montal, M.

(2012) J Biol Chem 287: 43063-43070

• PubMed: 23095758 
• DOI: https://doi.org/10.1074/jbc.M112.415091
• Primary Citation of Related Structures:  
  4H33, 4H37


• PubMed Abstract: 
  

  Voltage-gated K(+) channels underlie the electrical excitability of cells. Each subunit of the functional tetramer consists of the tandem fusion of two modules, an N-terminal voltage-sensor and a C-terminal pore. To investigate how sensor coupling to the pore generates voltage-dependent channel opening, we solved the crystal structure and characterized the function of a voltage-gated K(+) channel pore in a lipid membrane. The structure of a functional channel in a membrane environment at 3.1 Å resolution establishes an unprecedented connection between channel structure and function. The structure is unique in delineating an ion-occupied ready to conduct selectivity filter, a confined aqueous cavity, and a closed activation gate, embodying a dynamic entity trapped in an unstable closed state.

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Organizational Affiliation: 

Section of Neurobiology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, 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)

Macromolecule Content

• Total Structure Weight: 31.28 kDa 
• Atom Count: 1,307 
• Modelled Residue Count: 172 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo2059 protein	A, B	137	Listeria monocytogenes EGD-e	Mutation(s): 1  Gene Names: lmo2059 Membrane Entity: Yes
UniProt
Find proteins for Q8Y5K1 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y5K1  Go to UniProtKB:  Q8Y5K1

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 0.341 
• R-Value Work: 0.314 
• R-Value Observed: 0.318 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.1	α = 90
b = 80.67	β = 90
c = 55.522	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): Santos, J.S., Asmar-Rovira, G.A., Han, G.W., Liu, W., Syeda, R., Cherezov, V., Baker, K.A., Stevens, R.C., Montal, M.

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2013-01-16
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description