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- PDB-6w7b: K2P2.1 (TREK-1), 0 mM K+ -

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Basic information

Entry
Database: PDB / ID: 6w7b
TitleK2P2.1 (TREK-1), 0 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
heptyl beta-D-glucopyranoside / : / DECANE / DODECANE / : / N-OCTANE / Potassium channel subfamily K member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.88 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 19, 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)70,07113
Polymers68,6082
Non-polymers1,46311
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13180 Å2
ΔGint-81 kcal/mol
Surface area31410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.906, 122.597, 125.576
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 / Sugars , 2 types, 3 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
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
#5: Sugar ChemComp-B7G / heptyl beta-D-glucopyranoside / HEPTYL-BETA-D-GLUCOPYRANOSIDE / heptyl beta-D-glucoside / heptyl D-glucoside / heptyl glucoside


Type: D-saccharide / Mass: 278.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
heptyl-b-D-GlucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 10 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26
#4: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: 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 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: 3.75 Å3/Da / Density % sol: 67.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
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 PILATUS3 6M / Detector: PIXEL / Date: Jan 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.88→45.8 Å / Num. obs: 10002 / % possible obs: 99.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.196 / Net I/σ(I): 2.95
Reflection shellResolution: 3.88→4 Å / Num. unique obs: 2771 / CC1/2: 0.264

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
Cootmodel building
XDSdata scaling
PHASERphasing
Aimlessdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CQ6

6cq6


Resolution: 3.88→14.96 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.76
RfactorNum. reflection% reflectionSelection details
Rfree0.3087 490 -RANDOM
Rwork0.2747 ---
obs0.2764 9774 99.2 %-
Displacement parametersBiso mean: 248.2 Å2
Baniso -1Baniso -2Baniso -3
1--55.7923 Å20 Å20 Å2
2--32.0708 Å20 Å2
3---23.7215 Å2
Refine analyzeLuzzati coordinate error obs: 1.19 Å
Refinement stepCycle: LAST / Resolution: 3.88→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4083 0 85 0 4168
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0064250HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.845747HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1419SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes671HARMONIC5
X-RAY DIFFRACTIONt_it4175HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion589SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4039SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion7.51
X-RAY DIFFRACTIONt_other_torsion12.55
LS refinement shellResolution: 3.88→3.93 Å
RfactorNum. reflection% reflection
Rfree0.2594 15 -
Rwork0.2808 --
obs0.28 408 98.31 %
Refinement TLS params.

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)
10.9707-0.35880.11220.5730.28851.818-0.00380.03150.00740.03150.025-0.06580.0074-0.0658-0.02120.03230.0219-0.0107-0.00010.00080.0021-0.8537-23.6583-21.2663
21.0157-0.51851.27832.1241.27832.750.00380.01020.04770.01020.0125-0.00020.0477-0.0002-0.01630.04420.0137-0.01290.01230.00250.00554.904-27.4613-33.8469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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