6V37 | pdb_00006v37

K2P2.1(TREK-1)I110D:RuR:ML335 bound channel structure

• PDB DOI: https://doi.org/10.2210/pdb6V37/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus
• Expression System: Komagataella pastoris
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2019-11-25 Released: 2020-02-26 
• Deposition Author(s): Pope, L., Lolicato, M., Minor, D.L.
• Funding Organization(s): National Institutes of Health/National Library of Medicine (NIH/NLM)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.317 (Depositor), 0.371 (DCC) 
• R-Value Work: 
  0.272 (Depositor), 0.298 (DCC) 
• R-Value Observed: 
  0.274 (Depositor) 

Starting Model: experimental

Literature

Polynuclear Ruthenium Amines Inhibit K2PChannels via a "Finger in the Dam" Mechanism.

Pope, L., Lolicato, M., Minor Jr., D.L.

(2020) Cell Chem Biol 

• PubMed: 32059793 
• DOI: https://doi.org/10.1016/j.chembiol.2020.01.011
• Primary Citation Related Structures: 
  6V36, 6V37, 6V3C, 6V3I


• PubMed Abstract: 
  

  The trinuclear ruthenium amine ruthenium red (RuR) inhibits diverse ion channels, including K _2P potassium channels, TRPs, the calcium uniporter, CALHMs, ryanodine receptors, and Piezos. Despite this extraordinary array, there is limited information for how RuR engages targets. Here, using X-ray crystallographic and electrophysiological studies of an RuR-sensitive K _2P , K _2P 2.1 (TREK-1) I110D, we show that RuR acts by binding an acidic residue pair comprising the "Keystone inhibitor site" under the K _2P CAP domain archway above the channel pore. We further establish that Ru360, a dinuclear ruthenium amine not known to affect K _2P s, inhibits RuR-sensitive K _2P s using the same mechanism. Structural knowledge enabled a generalizable design strategy for creating K _2P RuR "super-responders" having nanomolar sensitivity. Together, the data define a "finger in the dam" inhibition mechanism acting at a novel K _2P inhibitor binding site. These findings highlight the polysite nature of K _2P pharmacology and provide a new framework for K _2P inhibitor development.

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Organizational Affiliation: 
• Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA.
Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA; Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, CA 93858-2330, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 93858-2330, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 93858-2330, USA; Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: [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: gel filtration

Macromolecule Content 

• Total Structure Weight: 71.22 kDa 
• Atom Count: 4,309 
• Modeled Residue Count: 534 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium channel subfamily K member 2	A, B	312	Mus musculus	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P97438 (Mus musculus) Explore P97438  Go to UniProtKB:  P97438
IMPC:  MGI:109366

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R2R (Subject of Investigation/LOI)	C [auth A]	ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2) H28 N14 O2 Ru3 FOOPNNMQSUSGAT-UHFFFAOYSA-N
Q6F	H [auth A], P [auth B]	N-[(2,4-dichlorophenyl)methyl]-4-[(methylsulfonyl)amino]benzamide C15 H14 Cl2 N2 O3 S RDFIQTZRJRVFHK-UHFFFAOYSA-N
D12	E [auth A], F [auth A], G [auth A], O [auth B]	DODECANE C12 H26 SNRUBQQJIBEYMU-UHFFFAOYSA-N
CD	D [auth A], N [auth B], R [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
HEX	M [auth B]	HEXANE C6 H14 VLKZOEOYAKHREP-UHFFFAOYSA-N
K	I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.317 (Depositor), 0.371 (DCC) 
• R-Value Work:  0.272 (Depositor), 0.298 (DCC) 
• R-Value Observed: 0.274 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.018	α = 90
b = 118.735	β = 90
c = 129.036	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Pope, L., Lolicato, M., Minor, D.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	NIH-R01-MH093603

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary