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- PDB-6w84: K2P2.1 (TREK-1), 200 mM K+ -

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Basic information

Entry
Database: PDB / ID: 6w84
TitleK2P2.1 (TREK-1), 200 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
: / DODECANE / : / N-OCTANE / Potassium channel subfamily K member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 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 1.2Oct 23, 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)69,93615
Polymers68,6082
Non-polymers1,32813
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12060 Å2
ΔGint-95 kcal/mol
Surface area31340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.627, 121.287, 130.034
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 170.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
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: 4.06 Å3/Da / Density % sol: 69.7 %
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

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
2451N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.0332
SYNCHROTRONDiamond I2322.75
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELMay 10, 2018
DECTRIS PILATUS 12M2PIXELMar 1, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2Silicon crystal
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
22.751
ReflectionResolution: 3.7→47.83 Å / Num. obs: 12454 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 7.1
Reflection shellResolution: 3.7→4.05 Å / Num. unique obs: 2880 / CC1/2: 0.12

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
GDA2.11.4data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6cq6

6cq6


Resolution: 3.7→14.99 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.714
RfactorNum. reflection% reflectionSelection details
Rfree0.3337 533 -RANDOM
Rwork0.2626 ---
obs0.266 12196 99.9 %-
Displacement parametersBiso mean: 253.28 Å2
Baniso -1Baniso -2Baniso -3
1--34.8176 Å20 Å20 Å2
2--20.6085 Å20 Å2
3---14.2091 Å2
Refine analyzeLuzzati coordinate error obs: 0.84 Å
Refinement stepCycle: LAST / Resolution: 3.7→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4289 0 64 0 4353
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0054447HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.756026HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1484SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes713HARMONIC5
X-RAY DIFFRACTIONt_it4396HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion607SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4283SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion6.2
X-RAY DIFFRACTIONt_other_torsion11.76
LS refinement shellResolution: 3.7→3.75 Å
RfactorNum. reflection% reflection
Rfree0.1794 22 -
Rwork0.2452 --
obs0.2423 470 97.51 %
Refinement TLS params.Method: refined / Origin x: 1.611 Å / Origin y: -24.1846 Å / Origin z: -27.5526 Å
111213212223313233
T1.0146 Å2-0.0457 Å2-0.0489 Å2-1.304 Å20.0004 Å2--1.3275 Å2
L2.1385 °20.1558 °2-0.4213 °2-2.2946 °20.5823 °2--3.7007 °2
S-0.0121 Å °-0.0254 Å °0.366 Å °-0.0254 Å °0.0827 Å °-0.3651 Å °0.366 Å °-0.3651 Å °-0.0705 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|43 - A|321 A|401 - A|402 A|403 - A|405 A|406 - A|410 B|401 - B|401 B|35 - B|316 B|403 - B|403 B|402 - B|402 }A43 - 321
2X-RAY DIFFRACTION1{ A|43 - A|321 A|401 - A|402 A|403 - A|405 A|406 - A|410 B|401 - B|401 B|35 - B|316 B|403 - B|403 B|402 - B|402 }A401 - 402
3X-RAY DIFFRACTION1{ A|43 - A|321 A|401 - A|402 A|403 - A|405 A|406 - A|410 B|401 - B|401 B|35 - B|316 B|403 - B|403 B|402 - B|402 }A403 - 405
4X-RAY DIFFRACTION1{ A|43 - A|321 A|401 - A|402 A|403 - A|405 A|406 - A|410 B|401 - B|401 B|35 - B|316 B|403 - B|403 B|402 - B|402 }A406 - 410
5X-RAY DIFFRACTION1{ A|43 - A|321 A|401 - A|402 A|403 - A|405 A|406 - A|410 B|401 - B|401 B|35 - B|316 B|403 - B|403 B|402 - B|402 }B401
6X-RAY DIFFRACTION1{ A|43 - A|321 A|401 - A|402 A|403 - A|405 A|406 - A|410 B|401 - B|401 B|35 - B|316 B|403 - B|403 B|402 - B|402 }B35 - 316
7X-RAY DIFFRACTION1{ A|43 - A|321 A|401 - A|402 A|403 - A|405 A|406 - A|410 B|401 - B|401 B|35 - B|316 B|403 - B|403 B|402 - B|402 }B403
8X-RAY DIFFRACTION1{ A|43 - A|321 A|401 - A|402 A|403 - A|405 A|406 - A|410 B|401 - B|401 B|35 - B|316 B|403 - B|403 B|402 - B|402 }B402

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