6W8C | pdb_00006w8c

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.263 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.251 (Depositor), 0.261 (DCC) 
  • R-Value Observed: 
    0.252 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6W8C

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1126/sciadv.abc9174
  • Primary Citation Related Structures: 
    6W7B, 6W7C, 6W7D, 6W7E, 6W82, 6W83, 6W84, 6W85, 6W86, 6W87, 6W88, 6W8A, 6W8C, 6W8F

  • 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. 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
    • Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA.

Macromolecule Content 

  • Total Structure Weight: 74.98 kDa 
  • Atom Count: 4,741 
  • Modeled Residue Count: 557 
  • Deposited Residue Count: 624 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Potassium channel subfamily K member 2
A, B
312Mus 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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97438
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IEP

Query on IEP



Download:Ideal Coordinates CCD File
AA [auth B],
L [auth A]
[(2~{S})-1-octadecanoyloxy-3-[oxidanyl-[(1~{R},2~{R},3~{S},4~{S},5~{S},6~{S})-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] icosa-5,8,11,14-tetraenoate
C47 H85 O19 P3
CNWINRVXAYPOMW-UWUKCHIJSA-N
Q6F

Query on Q6F



Download:Ideal Coordinates CCD File
CA [auth B],
J [auth A]
N-[(2,4-dichlorophenyl)methyl]-4-[(methylsulfonyl)amino]benzamide
C15 H14 Cl2 N2 O3 S
RDFIQTZRJRVFHK-UHFFFAOYSA-N
B7G

Query on B7G



Download:Ideal Coordinates CCD File
K [auth A],
W [auth B],
X [auth B],
Y [auth B]
heptyl beta-D-glucopyranoside
C13 H26 O6
NIDYWHLDTIVRJT-UJPOAAIJSA-N
R16

Query on R16



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A]
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
11A

Query on 11A



Download:Ideal Coordinates CCD File
BA [auth B],
M [auth A]
UNDECANOIC ACID
C11 H22 O2
ZDPHROOEEOARMN-UHFFFAOYSA-N
D12

Query on D12



Download:Ideal Coordinates CCD File
U [auth B],
V [auth B]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
UND

Query on UND



Download:Ideal Coordinates CCD File
Z [auth B]UNDECANE
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
OCT

Query on OCT



Download:Ideal Coordinates CCD File
S [auth B],
T [auth B]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
CD

Query on CD



Download:Ideal Coordinates CCD File
P [auth B],
Q [auth B],
R [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
LNK

Query on LNK



Download:Ideal Coordinates CCD File
DA [auth B]PENTANE
C5 H12
OFBQJSOFQDEBGM-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
N [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
N [auth A],
O [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.263 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.251 (Depositor), 0.261 (DCC) 
  • R-Value Observed: 0.252 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.129α = 90
b = 119.783β = 90
c = 128.872γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
GDAdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary