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- PDB-6rv4: Crystal structure of the human two pore domain potassium ion chan... -

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Basic information

Entry
Database: PDB / ID: 6rv4
TitleCrystal structure of the human two pore domain potassium ion channel TASK-1 (K2P3.1) in a closed conformation with a bound inhibitor BAY 2341237
ComponentsPotassium channel subfamily K member 3
KeywordsMEMBRANE PROTEIN / potassium channel / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


open rectifier potassium channel activity / TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / regulation of resting membrane potential / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / S100 protein binding / cellular response to zinc ion / cochlea development ...open rectifier potassium channel activity / TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / regulation of resting membrane potential / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / S100 protein binding / cellular response to zinc ion / cochlea development / negative regulation of cytosolic calcium ion concentration / potassium channel activity / potassium ion transmembrane transport / monoatomic ion transmembrane transport / potassium ion transport / monoatomic ion channel activity / cellular response to hypoxia / chemical synaptic transmission / response to xenobiotic stimulus / synapse / plasma membrane
Similarity search - Function
Potassium channel subfamily K member 3 / Two pore domain potassium channel, TASK family / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Chem-KKZ / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / CHOLESTEROL HEMISUCCINATE / Potassium channel subfamily K member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRodstrom, K.E.J. / Pike, A.C.W. / Zhang, W. / Quigley, A. / Speedman, D. / Mukhopadhyay, S.M.M. / Shrestha, L. / Chalk, R. / Venkaya, S. / Bushell, S.R. ...Rodstrom, K.E.J. / Pike, A.C.W. / Zhang, W. / Quigley, A. / Speedman, D. / Mukhopadhyay, S.M.M. / Shrestha, L. / Chalk, R. / Venkaya, S. / Bushell, S.R. / Tessitore, A. / Burgess-Brown, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust106169/Z/14/Z United Kingdom
European Commission115766 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N009274/1 United Kingdom
CitationJournal: Nature / Year: 2020
Title: A lower X-gate in TASK channels traps inhibitors within the vestibule.
Authors: Rodstrom, K.E.J. / Kiper, A.K. / Zhang, W. / Rinne, S. / Pike, A.C.W. / Goldstein, M. / Conrad, L.J. / Delbeck, M. / Hahn, M.G. / Meier, H. / Platzk, M. / Quigley, A. / Speedman, D. / ...Authors: Rodstrom, K.E.J. / Kiper, A.K. / Zhang, W. / Rinne, S. / Pike, A.C.W. / Goldstein, M. / Conrad, L.J. / Delbeck, M. / Hahn, M.G. / Meier, H. / Platzk, M. / Quigley, A. / Speedman, D. / Shrestha, L. / Mukhopadhyay, S.M.M. / Burgess-Brown, N.A. / Tucker, S.J. / Muller, T. / Decher, N. / Carpenter, E.P.
History
DepositionMay 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 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_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

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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 3
B: Potassium channel subfamily K member 3
C: Potassium channel subfamily K member 3
D: Potassium channel subfamily K member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,89424
Polymers120,4684
Non-polymers7,42620
Water00
1
A: Potassium channel subfamily K member 3
B: Potassium channel subfamily K member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,43413
Polymers60,2342
Non-polymers4,20011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12600 Å2
ΔGint-120 kcal/mol
Surface area24000 Å2
MethodPISA
2
C: Potassium channel subfamily K member 3
D: Potassium channel subfamily K member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,46011
Polymers60,2342
Non-polymers3,2269
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12900 Å2
ΔGint-122 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.100, 201.330, 238.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Potassium channel subfamily K member 3 / Acid-sensitive potassium channel protein TASK-1 / TWIK-related acid-sensitive K(+) channel 1 / Two ...Acid-sensitive potassium channel protein TASK-1 / TWIK-related acid-sensitive K(+) channel 1 / Two pore potassium channel KT3.1 / Two pore K(+) channel KT3.1


Mass: 30117.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Two-pore domain potassium channel K2P3.1 (TASK-1) / Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK3, TASK, TASK1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14649
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H50O4
#4: Chemical ChemComp-KKZ / [4-[[2-(4-chlorophenyl)imidazo[1,2-a]pyridin-3-yl]methyl]piperazin-1-yl]-[6-(trifluoromethyloxy)pyridin-2-yl]methanone


Mass: 515.915 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H21ClF3N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.64 Å3/Da / Density % sol: 73.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TRIS pH 8.5, 0.05 M KCl, 31% v/v PEG400, 3% w/v sucrose
Temp details: Ambient

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.099→43.116 Å / Num. obs: 33101 / % possible obs: 80.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 61.74 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.153 / Rrim(I) all: 0.219 / Net I/σ(I): 6.6
Reflection shellResolution: 3.099→3.232 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1654 / CC1/2: 0.792 / Rpim(I) all: 0.348 / Rrim(I) all: 0.702 / % possible all: 34.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSVERSION Jan 26, 2018data reduction
XDSVERSION Jan 26, 2018data scaling
STARANISO2.2.19data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BW5

4bw5


Resolution: 3.1→41.16 Å / Cor.coef. Fo:Fc: 0.801 / Cor.coef. Fo:Fc free: 0.826 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.419
Details: REFINED AGAINST STARANISO ANISOTROPICALLY TRUNCAED DATA. POSITIVE DIFFRERENCE PEAKS FOR WATER MOLECULES WERE SEEN, CORRESPONDING TO WATER POSITIONS IN 6RV2 and 6RV3, BUT WERE NOT MODELLED AT THIS RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1587 4.8 %RANDOM
Rwork0.25 ---
obs0.251 33045 80.9 %-
Displacement parametersBiso mean: 48.81 Å2
Baniso -1Baniso -2Baniso -3
1--6.94 Å20 Å20 Å2
2--5.7793 Å20 Å2
3---1.1607 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: LAST / Resolution: 3.1→41.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7985 0 405 0 8390
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088585HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.911657HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3013SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1402HARMONIC5
X-RAY DIFFRACTIONt_it8585HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.95
X-RAY DIFFRACTIONt_other_torsion17.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1131SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance64HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10109SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.15 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2138 -3.33 %
Rwork0.2653 639 -
all0.2635 661 -
obs--32.71 %
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)Origin x (Å)Origin y (Å)Origin z (Å)
12.7745-0.22260.17762.0745-0.40832.41880.07710.1962-0.1295-0.1747-0.0421-0.0440.06770.1007-0.035-0.2828-0.00180.01980.02770.2076-0.09922.7485-41.21525.5404
22.84220.2642-0.16121.1679-0.62022.11810.0797-0.02670.1217-0.043-0.0510.1805-0.0504-0.1452-0.0287-0.2233-0.0133-0.0399-0.0070.1969-0.034-8.6706-37.241829.0082
33.46180.08230.64972.6158-0.76532.2062-0.02210.18910.2304-0.133-0.05930.1753-0.0625-0.23060.0814-0.32980.03050.03640.00330.0497-0.1193-25.12622.442433.3418
42.90840.0551-0.06282.18910.04482.2573-0.0431-0.0615-0.0249-0.12960.1215-0.04460.10580.1286-0.0784-0.27340.00670.03660.00230.0891-0.0574-13.579518.361936.767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 304}
2X-RAY DIFFRACTION2{B|1 - 261}
3X-RAY DIFFRACTION3{C|1 - 304}
4X-RAY DIFFRACTION4{D|1 - 261}

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