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- PDB-8uf6: Structure of Trek-1(K2P2.1) with ML336 -

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Basic information

Entry
Database: PDB / ID: 8uf6
TitleStructure of Trek-1(K2P2.1) with ML336
ComponentsPotassium channel subfamily K member 2
KeywordsMEMBRANE PROTEIN / membrane preotein / ML335 / trek1 / trek-1 / malemide / trek-1 ligand / crystal / trans-membrane protein / transmembrane protein / k2p / two pore potassium channel / potassium channel / KCNK2 / Potassium channel subfamily K member 2 / ML336 / LH9
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
Chem-16C / : / DECANE / DODECANE / : / N-OCTANE / HEXADECANE / : / Potassium channel subfamily K member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLolicato, M. / Mondal, A. / Minor, D.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01-MH116278 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01-MH093603 United States
CitationJournal: To Be Published
Title: Structure of Trek-1(K2P2.1) with ML336
Authors: Lolicato, M. / Mondal, A. / Minor, D.L.
History
DepositionOct 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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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)66,50921
Polymers63,1242
Non-polymers3,38619
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.953, 118.597, 130.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 31561.848 Da / Num. of mol.: 2 / Fragment: residues 35-321
Mutation: various mutations made for stability and better protein expression for structural studies
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 , 9 types, 19 molecules

#2: Chemical ChemComp-WRZ / N-[(2,4-dichlorophenyl)methyl]-4-propanamidobenzamide


Mass: 351.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16Cl2N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#5: 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.: 2 / Source method: obtained synthetically / Formula: C34H67NO3
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#9: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#10: Chemical ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34

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Details

Has ligand of interestY

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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: 4.29 Å3/Da / Density % sol: 71.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 20-25% PEG4000, 200 mM KCl, 100mM HEPES pH 7.0-7.5, 1mM CdCl2
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.9→14.9 Å / Num. obs: 23483 / % possible obs: 97.97 % / Redundancy: 7.2 % / CC1/2: 0.997 / Net I/σ(I): 8.7
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 16472 / CC1/2: 0.209

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→14.9 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3132 1114 4.79 %
Rwork0.2665 --
obs0.2687 23269 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4277 0 210 0 4487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044578
X-RAY DIFFRACTIONf_angle_d0.836169
X-RAY DIFFRACTIONf_dihedral_angle_d15.6871604
X-RAY DIFFRACTIONf_chiral_restr0.05707
X-RAY DIFFRACTIONf_plane_restr0.006737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.34921320.3522620X-RAY DIFFRACTION95
3.03-3.190.3691450.33652724X-RAY DIFFRACTION99
3.19-3.390.36931300.3182755X-RAY DIFFRACTION100
3.39-3.650.33331460.28192748X-RAY DIFFRACTION100
3.65-4.010.27821340.25182770X-RAY DIFFRACTION99
4.01-4.570.28331220.23492821X-RAY DIFFRACTION100
4.57-5.70.3421400.25382829X-RAY DIFFRACTION99
5.71-14.90.29381650.26372888X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -2.2258 Å / Origin y: -22.8627 Å / Origin z: 27.2198 Å
111213212223313233
T0.4918 Å20.0197 Å20.0073 Å2-0.5193 Å2-0.0658 Å2--0.4615 Å2
L1.8522 °20.0395 °20.0503 °2-1.4724 °20.0583 °2--1.8166 °2
S-0.0401 Å °-0.09 Å °-0.2556 Å °-0.0688 Å °0.1912 Å °-0.0897 Å °0.2345 Å °0.3234 Å °-0.1055 Å °
Refinement TLS groupSelection details: all

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