6W8F

K2P2.1 (TREK-1):ML335 complex, 0 mM K+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

K 2P channel C-type gating involves asymmetric selectivity filter order-disorder transitions.

Lolicato, M.Natale, A.M.Abderemane-Ali, F.Crottes, D.Capponi, S.Duman, R.Wagner, A.Rosenberg, J.M.Grabe, M.Minor Jr., D.L.

(2020) Sci Adv 6

  • DOI: 10.1126/sciadv.abc9174
  • Primary Citation of Related Structures:  
    6W82, 6W84, 6W83, 6W86, 6W85, 6W7C, 6W7B, 6W7E, 6W7D, 6W8A

  • PubMed Abstract: 
  • K 2P potassium channels regulate cellular excitability using their selectivity filter (C-type) gate. C-type gating mechanisms, best characterized in homotetrameric potassium channels, remain controversial and are attributed to selectivity filter pinching, dilation, or subtle structural changes ...

    K 2P potassium channels regulate cellular excitability using their selectivity filter (C-type) gate. C-type gating mechanisms, best characterized in homotetrameric potassium channels, remain controversial and are attributed to selectivity filter pinching, dilation, or subtle structural changes. The extent to which such mechanisms control C-type gating of innately heterodimeric K 2P s is unknown. Here, combining K 2P 2.1 (TREK-1) x-ray crystallography in different potassium concentrations, potassium anomalous scattering, molecular dynamics, and electrophysiology, we uncover unprecedented, asymmetric, potassium-dependent conformational changes that underlie K 2P C-type gating. These asymmetric order-disorder transitions, enabled by the K 2P heterodimeric architecture, encompass pinching and dilation, disrupt the S1 and S2 ion binding sites, require the uniquely long K 2P SF2-M4 loop and conserved "M3 glutamate network," and are suppressed by the K 2P C-type gate activator ML335. These findings demonstrate that two distinct C-type gating mechanisms can operate in one channel and underscore the SF2-M4 loop as a target for K 2P channel modulator development.


    Organizational Affiliation

    Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Potassium channel subfamily K member 2A, B312Mus musculusMutation(s): 13 
Gene Names: Kcnk2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P97438 (Mus musculus)
Explore P97438 
Go to UniProtKB:  P97438
IMPC:  MGI:109366
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
16C
Query on 16C

Download Ideal Coordinates CCD File 
E [auth A]N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE
C34 H67 N O3
YDNKGFDKKRUKPY-TURZORIXSA-N
 Ligand Interaction
Q6F
Query on Q6F

Download Ideal Coordinates CCD File 
D [auth A], U [auth B]N-[(2,4-dichlorophenyl)methyl]-4-[(methylsulfonyl)amino]benzamide
C15 H14 Cl2 N2 O3 S
RDFIQTZRJRVFHK-UHFFFAOYSA-N
 Ligand Interaction
R16
Query on R16

Download Ideal Coordinates CCD File 
F [auth A] , G [auth A] , H [auth A] , N [auth B] , R [auth B] , S [auth B] , T [auth B] , V [auth B] , 
F [auth A],  G [auth A],  H [auth A],  N [auth B],  R [auth B],  S [auth B],  T [auth B],  V [auth B],  W [auth B]
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
 Ligand Interaction
D12
Query on D12

Download Ideal Coordinates CCD File 
X [auth B]DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download Ideal Coordinates CCD File 
K [auth A], O [auth B], P [auth B], Q [auth B]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
LNK
Query on LNK

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L [auth A]PENTANE
C5 H12
OFBQJSOFQDEBGM-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A], I [auth A], J [auth A], M [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.671α = 90
b = 119.963β = 90
c = 128.941γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesNIH-R01-MH093603

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release