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- PDB-4xdl: Crystal structure of human two pore domain potassium ion channel ... -

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Basic information

Entry
Database: PDB / ID: 4xdl
TitleCrystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1) in complex with a brominated fluoxetine derivative.
ComponentsPotassium channel subfamily K member 10
KeywordsTRANSPORT PROTEIN / OUTWARD RECTIFICATION / MEMBRANE PROTEIN / K2P / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


TWIK related potassium channel (TREK) / cellular response to arachidonate / mechanosensitive potassium channel activity / Phase 4 - resting membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / monoatomic ion channel complex / potassium channel activity / potassium ion transmembrane transport / signal transduction / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TREK / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-40D / : / : / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Potassium channel subfamily K member 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsMackenzie, A. / Pike, A.C.W. / Dong, Y.Y. / Mukhopadhyay, S. / Ruda, G.F. / Brennan, P.E. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Burgess-Brown, N.A. ...Mackenzie, A. / Pike, A.C.W. / Dong, Y.Y. / Mukhopadhyay, S. / Ruda, G.F. / Brennan, P.E. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Burgess-Brown, N.A. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust092809/Z/10/Z United Kingdom
CitationJournal: Science / Year: 2015
Title: K2P channel gating mechanisms revealed by structures of TREK-2 and a complex with Prozac.
Authors: 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, ...Authors: 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.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Jan 10, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potassium channel subfamily K member 10
B: Potassium channel subfamily K member 10
C: Potassium channel subfamily K member 10
D: Potassium channel subfamily K member 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,41320
Polymers124,2404
Non-polymers5,17316
Water00
1
A: Potassium channel subfamily K member 10
B: Potassium channel subfamily K member 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,70710
Polymers62,1202
Non-polymers2,5868
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-116 kcal/mol
Surface area24240 Å2
MethodPISA
2
C: Potassium channel subfamily K member 10
D: Potassium channel subfamily K member 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,70710
Polymers62,1202
Non-polymers2,5868
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10790 Å2
ΔGint-115 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.710, 109.840, 166.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Potassium channel subfamily K member 10 / Outward rectifying potassium channel protein TREK-2 / TREK-2 K(+) channel subunit


Mass: 31060.111 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 67-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK10, TREK2 / Plasmid: PFB-CT10HF-LIC / Cell (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P57789
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-40D / 3-[2-bromanyl-4-(trifluoromethyl)phenoxy]-N-methyl-3-phenyl-propan-1-amine


Mass: 388.222 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H17BrF3NO
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M KCl, 0.1M MES pH 6.5, 0.05M magnesium chloride, 0.001M cadmium chloride, 18% (v/v) PEG500 Dimethylether

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.8856 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 3.5→39.07 Å / Num. obs: 24216 / % possible obs: 99.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 122.95 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 17.5
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.846 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XDJ

4xdj


Resolution: 3.5→35 Å / Cor.coef. Fo:Fc: 0.8873 / Cor.coef. Fo:Fc free: 0.8842 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.499
Details: BOUND BR-FLUOXETINE LIGAND IS ONLY PARTIALLY RESOLVED IN ELECTRON DENSITY AND ONLY BROMINATED TRIFLUOROMETHYL PHENOXY PORTION HAS BEEN INCLUDED IN THE MODEL. OCCUPANCY OF BROMINE ATOM HAS ...Details: BOUND BR-FLUOXETINE LIGAND IS ONLY PARTIALLY RESOLVED IN ELECTRON DENSITY AND ONLY BROMINATED TRIFLUOROMETHYL PHENOXY PORTION HAS BEEN INCLUDED IN THE MODEL. OCCUPANCY OF BROMINE ATOM HAS BEEN REDUCED TO 0.8 TO ACCOUNT FOR EFFECTS OF RADIATION DAMAGE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2633 1217 5.04 %RANDOM
Rwork0.2352 ---
obs0.2366 24155 99.95 %-
Displacement parametersBiso mean: 157.05 Å2
Baniso -1Baniso -2Baniso -3
1-14.1713 Å20 Å20 Å2
2--9.5949 Å20 Å2
3----23.7662 Å2
Refine analyzeLuzzati coordinate error obs: 1.023 Å
Refinement stepCycle: 1 / Resolution: 3.5→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7474 0 92 0 7566
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097755HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9310624HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3244SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes104HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1168HARMONIC5
X-RAY DIFFRACTIONt_it7755HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.95
X-RAY DIFFRACTIONt_other_torsion2.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1069SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9571SEMIHARMONIC4
LS refinement shellResolution: 3.5→3.65 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.245 127 4.37 %
Rwork0.2237 2778 -
all0.2246 2905 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
17.2096-2.40610.25453.3858-0.07452.4510.17380.63080.7089-0.4654-0.3821-0.1775-0.3705-0.0680.2083-0.22410.1045-0.0275-0.4023-0.0122-0.3583Chain A0.7823140.73816.5047
25.3413-1.8637-0.763.05010.87142.2882-0.113-0.83670.43170.1587-0.0864-0.2466-0.35940.14130.1994-0.29640.0381-0.098-0.2459-0.086-0.3458Chain B1.4583142.87529.7249
33.48122.3318-1.27656.0855-1.14183.8486-0.17420.03340.90380.01920.57540.9587-0.63370.2509-0.4012-0.3004-0.3216-0.0103-0.25320.017-0.3592Chain C-7.6378193.417-16.0205
44.89362.6011-1.49494.8948-1.78132.31010.0136-0.35360.07940.0029-0.2112-0.13650.02590.63210.1976-0.2696-0.25530.0142-0.0541-0.0166-0.4962Chain D1.7006186.2-18.7909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{D|73 - 900}
2X-RAY DIFFRACTION2{B|73 - 900}
3X-RAY DIFFRACTION3{C|73 - 900}
4X-RAY DIFFRACTION4{D|73 - 900}

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