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- PDB-6w8a: K2P2.1 (TREK-1):ML335 complex, 10 mM K+ -

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Basic information

Entry
Database: PDB / ID: 6w8a
TitleK2P2.1 (TREK-1):ML335 complex, 10 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 / sarcolemma / postsynaptic density membrane / 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
Chem-16C / : / DODECANE / : / PENTANE / Chem-Q6F / HEXADECANE / Potassium channel subfamily K member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 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 13, 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)72,81825
Polymers68,6082
Non-polymers4,21023
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16100 Å2
ΔGint-168 kcal/mol
Surface area31030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.867, 119.951, 129.245
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 , 7 types, 23 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-16C / N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE / C16-CERAMIDE / N-PALMITOYL-D-ERYTHRO-SPHINGOSINE / (2S,3R,4E)-2-PALMITOYLAMINOOCTADEC-4-ENE-1,3-DIOL / (2S,3R,4E)-2-PALMITOYLAMINO-1,3-OCTADEC-4-ENEDIOL


Mass: 537.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H67NO3
#5: Chemical
ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H34 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#7: Chemical ChemComp-LNK / PENTANE


Mass: 72.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12
#8: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26

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Details

Has ligand of interestY
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: 3.78 Å3/Da / Density % sol: 67.44 %
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→46.47 Å / Num. obs: 21415 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 5.8
Reflection shellResolution: 3→3.18 Å / Num. unique obs: 3357 / CC1/2: 0.108

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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: 3.002→15 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.939 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.838 / SU Rfree Blow DPI: 0.355 / SU Rfree Cruickshank DPI: 0.367
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 1021 -RANDOM
Rwork0.2512 ---
obs0.2518 21163 99.7 %-
Displacement parametersBiso mean: 150.1 Å2
Baniso -1Baniso -2Baniso -3
1-21.0633 Å20 Å20 Å2
2---16.7241 Å20 Å2
3----4.3392 Å2
Refine analyzeLuzzati coordinate error obs: 0.62 Å
Refinement stepCycle: LAST / Resolution: 3.002→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4341 0 209 0 4550
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084647HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.846263HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1590SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes732HARMONIC5
X-RAY DIFFRACTIONt_it4647HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion618SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4296SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion6.25
X-RAY DIFFRACTIONt_other_torsion13.33
LS refinement shellResolution: 3.002→3.02 Å
RfactorNum. reflection% reflection
Rfree0.24 17 -
Rwork0.2497 --
obs--94.57 %
Refinement TLS params.Origin x: 2.5515 Å / Origin y: -23.4454 Å / Origin z: -27.2576 Å
111213212223313233
T0.8712 Å2-0.0209 Å20.0235 Å2-0.8321 Å20.0773 Å2--0.8735 Å2
L1.1864 °20.1237 °20.283 °2-1.4171 °2-0.4251 °2--2.03 °2
S-0.0847 Å °0.0826 Å °0.1799 Å °0.0826 Å °0.1697 Å °-0.1909 Å °0.1799 Å °-0.1909 Å °-0.085 Å °
Refinement TLS groupSelection details: { *|* }

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