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- PDB-6w8c: K2P2.1 (TREK-1):ML335 complex, 1 mM K+ -

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Basic information

Entry
Database: PDB / ID: 6w8c
TitleK2P2.1 (TREK-1):ML335 complex, 1 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 / positive regulation of cellular response to hypoxia / cardiac ventricle development / negative regulation of cardiac muscle cell proliferation / stabilization of membrane potential / potassium ion leak channel activity / astrocyte projection / potassium channel inhibitor activity / negative regulation of DNA biosynthetic process ...TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / positive regulation of cellular response to hypoxia / cardiac ventricle development / negative regulation of cardiac muscle cell proliferation / stabilization of membrane potential / potassium ion leak channel activity / astrocyte projection / potassium channel inhibitor activity / negative regulation of DNA biosynthetic process / outward rectifier potassium channel activity / cochlea development / voltage-gated potassium channel activity / calyx of Held / response to axon injury / axon terminus / response to mechanical stimulus / potassium ion transmembrane transport / voltage-gated potassium channel complex / regulation of membrane potential / potassium ion transport / memory / cellular response to hypoxia / apical plasma membrane / G protein-coupled receptor signaling pathway / axon / neuronal cell body / cell surface / endoplasmic reticulum / 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
UNDECANOIC ACID / heptyl beta-D-glucopyranoside / : / DODECANE / Chem-IEP / : / PENTANE / N-OCTANE / Chem-Q6F / HEXADECANE ...UNDECANOIC ACID / heptyl beta-D-glucopyranoside / : / DODECANE / Chem-IEP / : / PENTANE / N-OCTANE / Chem-Q6F / HEXADECANE / UNDECANE / Potassium channel subfamily K member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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

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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 2
B: Potassium channel subfamily K member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,98330
Polymers68,6082
Non-polymers6,37528
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17170 Å2
ΔGint-120 kcal/mol
Surface area31900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.129, 119.783, 128.872
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, 6 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
#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.: 4 / Source method: obtained synthetically / Formula: C13H26O6
IdentifierTypeProgram
heptyl-b-D-GlucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 11 types, 25 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-R16 / HEXADECANE / Hexadecane


Mass: 226.441 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34
#4: 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
#6: Chemical ChemComp-IEP / [(2~{S})-1-octadecanoyloxy-3-[oxidanyl-[(1~{R},2~{R},3~{S},4~{S},5~{S},6~{S})-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] icosa-5,8,11,14-tetraenoate


Mass: 1047.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H85O19P3
#7: Chemical ChemComp-11A / UNDECANOIC ACID / Undecylic acid


Mass: 186.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22O2 / Comment: antifungal*YM
#8: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#9: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#10: Chemical ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26
#11: Chemical ChemComp-UND / UNDECANE / LIPID FRAGMENT / Undecane


Mass: 156.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24
#12: Chemical ChemComp-LNK / PENTANE / Pentane


Mass: 72.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 67.43 %
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-D11.03321
SYNCHROTRONDiamond I2322.75
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELMar 23, 2017
DECTRIS PILATUS 12M2PIXELMar 4, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2silicon crystal
Radiation wavelength
IDWavelength (Å)Relative weight
11.033211
22.751
ReflectionResolution: 2.6→46.49 Å / Num. obs: 32731 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.7
Reflection shellResolution: 2.6→2.72 Å / Num. unique obs: 3898 / CC1/2: 0.192

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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: 2.6→14.97 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.386 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.365 / SU Rfree Blow DPI: 0.252 / SU Rfree Cruickshank DPI: 0.26
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 1581 -RANDOM
Rwork0.2512 ---
obs0.2518 32466 100 %-
Displacement parametersBiso mean: 122.17 Å2
Baniso -1Baniso -2Baniso -3
1-21.3513 Å20 Å20 Å2
2---13.5926 Å20 Å2
3----7.7588 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: LAST / Resolution: 2.6→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4341 0 399 1 4741
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0134828HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.466495HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1701SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes741HARMONIC5
X-RAY DIFFRACTIONt_it4828HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion651SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3887SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion6.95
X-RAY DIFFRACTIONt_other_torsion24.51
LS refinement shellResolution: 2.6→2.62 Å
RfactorNum. reflection% reflection
Rfree0.2184 33 -
Rwork0.2415 --
obs0.2403 650 100 %
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)
10.22970.11930.06740.2146-0.24760.2949-0.00040.00680.00040.00680.0031-0.00530.0004-0.0053-0.0027-0.0035-0.0026-0.0023-0.00030.0099-0.00080.6054-20.1158-20.3902
20.08540.0373-0.03070.2714-0.17310.1667-0.0001-0.00060.0021-0.00060.0014-0.00070.0021-0.0007-0.00130.0003-0.00350.0008-0.0030.0071-0.00174.5886-27.0159-33.8259
30.01180.008-0.01550.02890.00240.0081-0.00010.00030.00010.00030-0.00020.0001-0.00020-0.00020.0002-0.0010.00010.0005-0.000210.3433-12.1715-29.9115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|35 - A|321 }A35 - 321
2X-RAY DIFFRACTION2{ B|35 - B|316 }B35 - 316
3X-RAY DIFFRACTION3{ A|410 - A|410 B|414 - B|414 }A410
4X-RAY DIFFRACTION3{ A|410 - A|410 B|414 - B|414 }B414

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