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- PDB-6rv2: Crystal structure of the human two pore domain potassium ion chan... -

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Basic information

Entry
Database: PDB / ID: 6rv2
TitleCrystal structure of the human two pore domain potassium ion channel TASK-1 (K2P3.1) in a closed conformation
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 / stabilization of membrane potential / regulation of resting 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 / stabilization of membrane potential / regulation of resting 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
: / 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 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 / 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

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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)128,79626
Polymers120,4684
Non-polymers8,32822
Water55831
1
A: Potassium channel subfamily K member 3
B: Potassium channel subfamily K member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,88314
Polymers60,2342
Non-polymers4,64912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13530 Å2
ΔGint-122 kcal/mol
Surface area24430 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)63,91312
Polymers60,2342
Non-polymers3,67910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12950 Å2
ΔGint-124 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.140, 204.790, 238.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein / Sugars , 2 types, 7 molecules ABCD

#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
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK3, TASK, TASK1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14649
#4: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 4 types, 50 molecules

#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.: 7 / Source method: obtained synthetically / Formula: C31H50O4
#5: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 4.58 Å3/Da / Density % sol: 73.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TRIS pH 8.5, 0.05 M KCl, 32% 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: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3→47.668 Å / Num. obs: 36417 / % possible obs: 79.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 75.54 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.103 / Rrim(I) all: 0.239 / Net I/σ(I): 5.6
Reflection shellResolution: 3→3.12 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.021 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1822 / CC1/2: 0.697 / Rpim(I) all: 0.464 / Rrim(I) all: 1.124 / % possible all: 37.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSVERSION Jan 26, 2018data reduction
XSCALEVERSION Mar 15, 2019data scaling
STARANISO2.2.19data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BW5

4bw5


Resolution: 3→47.04 Å / Cor.coef. Fo:Fc: 0.808 / Cor.coef. Fo:Fc free: 0.841 / SU R Cruickshank DPI: 1.499 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.417 / SU Rfree Blow DPI: 0.392 / SU Rfree Cruickshank DPI: 0.4
Details: Refined against STARANISO anisotropically truncated data
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1756 4.83 %RANDOM
Rwork0.253 ---
obs0.254 36373 79.7 %-
Displacement parametersBiso mean: 66.77 Å2
Baniso -1Baniso -2Baniso -3
1--13.8238 Å20 Å20 Å2
2--10.7283 Å20 Å2
3---3.0955 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: LAST / Resolution: 3→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8009 0 426 31 8466
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088623HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.911696HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3090SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1405HARMONIC5
X-RAY DIFFRACTIONt_it8623HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.03
X-RAY DIFFRACTIONt_other_torsion17.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1155SEMIHARMONIC5
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_contact10204SEMIHARMONIC4
LS refinement shellResolution: 3→3.05 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2558 -5.36 %
Rwork0.2288 689 -
all0.2303 728 -
obs--35.86 %
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)
12.6606-0.49430.31031.6699-0.36952.19260.06010.0939-0.2428-0.1763-0.1832-0.11380.07860.1330.1231-0.39930.00510.01380.01250.1461-0.18572.8402-40.853525.7508
22.41650.05830.18291.1463-0.43291.37380.0148-0.01320.0371-0.0417-0.0520.2460.0482-0.20380.0372-0.3471-0.0089-0.00390.01290.1504-0.0825-8.4415-37.274429.3343
32.93760.13760.232.23-0.71732.1015-0.0490.05340.2297-0.1019-0.04820.075-0.0606-0.1080.0972-0.45370.02730.02940.03940.0184-0.1763-25.290122.81833.041
43.08780.1747-0.0611.6474-0.58852.273-0.0013-0.1963-0.02720.00710.1433-0.0460.03720.0922-0.142-0.41730.00840.0362-0.01310.0947-0.106-13.629719.102336.7996
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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