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

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Basic information

Entry
Database: PDB / ID: 4xdk
TitleCrystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1) in complex with norfluoxetine
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) / Phase 4 - resting membrane potential / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / monoatomic ion channel complex / potassium channel activity / potassium ion transmembrane transport / memory / 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-405 / Chem-408 / : / 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: 3.6 Å
AuthorsPike, A.C.W. / Dong, Y.Y. / Mackenzie, A. / Mukhopadhyay, S. / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.4Oct 23, 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)129,99822
Polymers124,2404
Non-polymers5,75818
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)66,57913
Polymers62,1202
Non-polymers4,45911
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11690 Å2
ΔGint-124 kcal/mol
Surface area23770 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)63,4199
Polymers62,1202
Non-polymers1,2987
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-91 kcal/mol
Surface area23220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.190, 113.030, 112.500
Angle α, β, γ (deg.)90.00, 90.41, 90.00
Int Tables number4
Space group name H-MP1211

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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-408 / (3R)-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine / (R)-Norfluoxetine


Mass: 295.300 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H16F3NO
#5: Chemical
ChemComp-405 / (3S)-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine / (S)-Norfluoxetine


Mass: 295.300 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H16F3NO
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: 3.85 Å3/Da / Density % sol: 68.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M KCl, 0.2M ammonium formate, 0.1M Tris pH 7, 31% pentaerythritol ethoxylate 15/04

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.6→39.87 Å / Num. obs: 21872 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 135.63 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.1
Reflection shellResolution: 3.6→3.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6

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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: 3.6→39.87 Å / Cor.coef. Fo:Fc: 0.8857 / Cor.coef. Fo:Fc free: 0.8886 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.498
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 1127 5.17 %RANDOM
Rwork0.2476 ---
obs0.2479 21816 99.44 %-
Displacement parametersBiso mean: 181.6 Å2
Baniso -1Baniso -2Baniso -3
1--54.5487 Å20 Å2-7.6376 Å2
2--24.8251 Å20 Å2
3---29.7236 Å2
Refine analyzeLuzzati coordinate error obs: 1.109 Å
Refinement stepCycle: 1 / Resolution: 3.6→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6921 0 214 0 7135
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097299HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.919991HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3015SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes80HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1114HARMONIC5
X-RAY DIFFRACTIONt_it7299HARMONIC20
X-RAY DIFFRACTIONt_nbd8SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.93
X-RAY DIFFRACTIONt_other_torsion2.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1017SEMIHARMONIC5
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_contact8917SEMIHARMONIC4
LS refinement shellResolution: 3.6→3.78 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2708 145 5.07 %
Rwork0.229 2716 -
all0.231 2861 -
obs--99.44 %
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)
11.8289-0.8058-1.20424.60872.65775.32430.31040.17710.1542-0.2473-0.52480.4062-0.0414-0.98870.2144-0.4638-0.1109-0.0078-0.2771-0.0526-0.3267Chain A9.225522.878858.6617
22.07850.48810.16245.04482.00876.22350.28160.13460.1951-0.1002-0.1705-0.52270.16870.4279-0.1111-0.4270.03990.1241-0.38590.0227-0.3197Chain B21.758323.715754.5983
30.75812.9726-1.984617.0232-8.71029.5417-0.03970.0767-0.42910.30760.33040.41561.0548-0.2279-0.2908-0.54820.12910.0934-0.37250.3855-0.2744Chain C54.283512.586-4.6315
41.1921.5422-2.21088.668-5.75168.9291-0.0482-0.1003-0.23281.4075-0.27540.471-0.25970.22850.3236-0.41940.12990.162-0.3760.4246-0.2041Chain D50.185520.8352.0362
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{D|73 - 901}
2X-RAY DIFFRACTION2{B|73 - 901}
3X-RAY DIFFRACTION3{C|73 - 901}
4X-RAY DIFFRACTION4{D|73 - 901}

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