4BW5 | pdb_00004bw5

Crystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1)

• PDB DOI: https://doi.org/10.2210/pdb4BW5/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2013-06-30 Released: 2013-07-31 
• Deposition Author(s): Pike, A.C.W., Dong, Y.Y., Dong, L., Quigley, A., Shrestha, L., Mukhopadhyay, S., Strain-Damerell, C., Goubin, S., Grieben, M., Shintre, C.A., Mackenzie, A., Vollmar, M., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Burgess-Brown, N., Carpenter, E.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.254 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Models: experimental

Literature

K2P Channel Gating Mechanisms Revealed by Structures of Trek-2 and a Complex with Prozac

Pike, A.C.W., 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.P., Tucker, S.J., Carpenter, E.P.

(2015) Science 347: 1256

• PubMed: 25766236 
• DOI: https://doi.org/10.1126/science.1261512
• Primary Citation 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.

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Organizational Affiliation: 
• Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK.
Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK. Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK.
Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK. OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK.
Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK. OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK. Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK. Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK.
Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK.
Pfizer Neusentis, Granta Park, Cambridge CB21 6GS, UK.
OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK. Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK. OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK. [e-mail] [e-mail].
Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK. OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK. [e-mail] [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 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 126.36 kDa 
• Atom Count: 7,235 
• Modeled Residue Count: 985 
• Deposited Residue Count: 1,128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POTASSIUM CHANNEL SUBFAMILY K MEMBER 10	A, B, C, D	282	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PC1	K [auth A], L [auth B]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H88 N O8 P NRJAVPSFFCBXDT-HUESYALOSA-N
CD	I [auth A], J [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
K	E [auth A], F [auth A], G [auth A], H [auth A], M [auth C], N [auth C], O [auth C], P [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.254 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.83	α = 90
b = 96.96	β = 92.58
c = 103.7	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-31 
Deposition Author(s): Pike, A.C.W., Dong, Y.Y., Dong, L., Quigley, A., Shrestha, L., Mukhopadhyay, S., Strain-Damerell, C., Goubin, S., Grieben, M., Shintre, C.A., Mackenzie, A., Vollmar, M., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Burgess-Brown, N., Carpenter, E.P.

Revision History  

• Version 1.0: 2013-07-31
  Type: Initial release
  
• Version 1.1: 2015-03-18
  Changes: Database references
• Version 1.2: 2015-03-25
  Changes: Database references
• Version 1.3: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary