4XDL

Crystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1) in complex with a brominated fluoxetine derivative.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

K2P channel gating mechanisms revealed by structures of TREK-2 and a complex with Prozac.

Dong, Y.Y.Pike, A.C.Mackenzie, A.McClenaghan, C.Aryal, P.Dong, L.Quigley, A.Grieben, M.Goubin, S.Mukhopadhyay, S.Ruda, G.F.Clausen, M.V.Cao, L.Brennan, P.E.Burgess-Brown, N.A.Sansom, M.S.Tucker, S.J.Carpenter, E.P.

(2015) Science 347: 1256-1259

  • DOI: https://doi.org/10.1126/science.1261512
  • Primary Citation of Related Structures:  
    4BW5, 4XDJ, 4XDK, 4XDL

  • PubMed Abstract: 

    TREK-2 (KCNK10/K2P10), a two-pore domain potassium (K2P) channel, is gated by multiple stimuli such as stretch, fatty acids, and pH and by several drugs. However, the mechanisms that control channel gating are unclear. Here we present crystal structures of the human TREK-2 channel (up to 3.4 angstrom resolution) in two conformations and in complex with norfluoxetine, the active metabolite of fluoxetine (Prozac) and a state-dependent blocker of TREK channels. Norfluoxetine binds within intramembrane fenestrations found in only one of these two conformations. Channel activation by arachidonic acid and mechanical stretch involves conversion between these states through movement of the pore-lining helices. These results provide an explanation for TREK channel mechanosensitivity, regulation by diverse stimuli, and possible off-target effects of the serotonin reuptake inhibitor Prozac.


  • Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium channel subfamily K member 10
A, B, C, D
282Homo sapiensMutation(s): 0 
Gene Names: KCNK10TREK2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P57789 (Homo sapiens)
Explore P57789 
Go to UniProtKB:  P57789
PHAROS:  P57789
GTEx:  ENSG00000100433 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP57789
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1

Download Ideal Coordinates CCD File 
G [auth A],
J [auth A],
R [auth D],
S [auth D]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
40D
Query on 40D

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
P [auth C],
T [auth D]
3-[2-bromanyl-4-(trifluoromethyl)phenoxy]-N-methyl-3-phenyl-propan-1-amine
C17 H17 Br F3 N O
KZCOQBCCEHGWOG-UHFFFAOYSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
H [auth A],
Q [auth D]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
K [auth B]
M [auth C]
N [auth C]
E [auth A],
F [auth A],
K [auth B],
M [auth C],
N [auth C],
O [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.71α = 90
b = 109.84β = 90
c = 166.74γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom092809/Z/10/Z

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Database references
  • Version 1.2: 2018-01-10
    Changes: Structure summary
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary