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- PDB-6w86: K2P2.1 (TREK-1):ML335 complex, 100 mM K+ -

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Basic information

Entry
Database: PDB / ID: 6w86
TitleK2P2.1 (TREK-1):ML335 complex, 100 mM K+
ComponentsPotassium channel subfamily K member 2
KeywordsMETAL TRANSPORT / ion channel / K2P / TREK1 / TREK-1
Function / homology
Function and homology information


TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / cellular response to arachidonate / mechanosensitive potassium channel activity / negative regulation of DNA biosynthetic process / positive regulation of cellular response to hypoxia / detection of mechanical stimulus involved in sensory perception of touch / chemical synaptic transmission, postsynaptic / stabilization of membrane potential / cardiac ventricle development ...TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / cellular response to arachidonate / mechanosensitive potassium channel activity / negative regulation of DNA biosynthetic process / positive regulation of cellular response to hypoxia / detection of mechanical stimulus involved in sensory perception of touch / chemical synaptic transmission, postsynaptic / stabilization of membrane potential / cardiac ventricle development / negative regulation of cardiac muscle cell proliferation / ligand-gated channel activity / potassium ion leak channel activity / node of Ranvier / outward rectifier potassium channel activity / glutamate secretion / astrocyte projection / regulation of synaptic transmission, GABAergic / cochlea development / voltage-gated potassium channel activity / response to axon injury / neuronal action potential / voltage-gated potassium channel complex / chloride transmembrane transport / calyx of Held / regulation of membrane potential / postsynaptic density membrane / sarcolemma / potassium ion transport / Schaffer collateral - CA1 synapse / memory / cellular response to hypoxia / apical plasma membrane / G protein-coupled receptor signaling pathway / protein heterodimerization activity / neuronal cell body / dendrite / cell surface / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TREK / Two pore domain potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
: / DECANE / DODECANE / : / PENTANE / N-OCTANE / Chem-Q6F / HEXADECANE / Potassium channel subfamily K member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.299 Å
AuthorsLolicato, M. / Minor, D.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)NIH-R01-MH093603 United States
CitationJournal: Sci Adv / Year: 2020
Title: K 2P channel C-type gating involves asymmetric selectivity filter order-disorder transitions.
Authors: Lolicato, M. / Natale, A.M. / Abderemane-Ali, F. / Crottes, D. / Capponi, S. / Duman, R. / Wagner, A. / Rosenberg, J.M. / Grabe, M. / Minor Jr., D.L.
History
DepositionMar 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel subfamily K member 2
B: Potassium channel subfamily K member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,49624
Polymers68,6082
Non-polymers2,88822
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14180 Å2
ΔGint-83 kcal/mol
Surface area32240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.317, 120.133, 129.431
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Potassium channel subfamily K member 2 / Outward rectifying potassium channel protein TREK-1 / TREK-1 K(+) channel subunit / Two pore ...Outward rectifying potassium channel protein TREK-1 / TREK-1 K(+) channel subunit / Two pore potassium channel TPKC1


Mass: 34303.938 Da / Num. of mol.: 2
Mutation: K84R, Q85E, T86K, I88L, A89R, Q90A, A92P, N95S, S96D, T97Q, N119A, S300A, E306A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnk2 / Production host: Komagataella pastoris (fungus) / References: UniProt: P97438

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Non-polymers , 8 types, 22 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-Q6F / N-[(2,4-dichlorophenyl)methyl]-4-[(methylsulfonyl)amino]benzamide


Mass: 373.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14Cl2N2O3S
#4: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical ChemComp-LNK / PENTANE


Mass: 72.149 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12
#6: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26
#7: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#8: Chemical ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34
#9: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.81 Å3/Da / Density % sol: 67.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22-25% PEG400, 100mM HEPES pH=8.0, 1mM CdCl2, 200mM KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.3→46.65 Å / Num. obs: 16146 / % possible obs: 98.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 4.9
Reflection shellResolution: 3.3→3.56 Å / Num. unique obs: 3319 / CC1/2: 0.163

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6cq6

6cq6


Resolution: 3.299→14.94 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.492
RfactorNum. reflection% reflectionSelection details
Rfree0.2876 899 -RANDOM
Rwork0.2504 ---
obs0.2526 15921 98.2 %-
Displacement parametersBiso mean: 146.44 Å2
Baniso -1Baniso -2Baniso -3
1-19.1545 Å20 Å20 Å2
2---24.9999 Å20 Å2
3---5.8454 Å2
Refine analyzeLuzzati coordinate error obs: 0.65 Å
Refinement stepCycle: LAST / Resolution: 3.299→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4341 0 167 0 4508
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114606HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.166219HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1551SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes730HARMONIC5
X-RAY DIFFRACTIONt_it4606HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion616SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3582SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion6.72
X-RAY DIFFRACTIONt_other_torsion17.68
LS refinement shellResolution: 3.3→3.32 Å
RfactorNum. reflection% reflection
Rfree0.2951 15 -
Rwork0.2263 --
obs0.2296 362 96.49 %
Refinement TLS params.

S13: 0.0005 Å ° / S31: 0.0005 Å ° / S33: -0.0013 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1759-0.01950.06150.0963-0.15430.1195-0.00020.00220.00220.0016-0.0019-0.0019-0.0009-0.0015-0.0009-0.00010.0041-00.3737-19.9054-20.5559
20.1478-0.139-0.05590.21140.0210.0945-0-0.0006-0.00060.0014-0.0009-0.00090.0005-0.00090.0011-0.00040.00340.00064.6798-26.8841-33.7985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|35 - A|321 A|401 - A|403 }A35 - 321
2X-RAY DIFFRACTION1{ A|35 - A|321 A|401 - A|403 }A401 - 403
3X-RAY DIFFRACTION2{ A|404 - A|405 B|35 - B|316 B|401 - B|404 }A404 - 405
4X-RAY DIFFRACTION2{ A|404 - A|405 B|35 - B|316 B|401 - B|404 }B35 - 316
5X-RAY DIFFRACTION2{ A|404 - A|405 B|35 - B|316 B|401 - B|404 }B401 - 404

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