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- PDB-8uec: Structure of TREK-1CG*:CAT335a -

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Basic information

Entry
Database: PDB / ID: 8uec
TitleStructure of TREK-1CG*:CAT335a
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 / CAT335a
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 / chemical synaptic transmission, postsynaptic / stabilization of membrane potential / negative regulation of cardiac muscle cell proliferation / potassium ion leak channel activity / 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 / chemical synaptic transmission, postsynaptic / stabilization of membrane potential / negative regulation of cardiac muscle cell proliferation / potassium ion leak channel activity / potassium channel inhibitor activity / negative regulation of DNA biosynthetic process / astrocyte projection / outward rectifier potassium channel activity / cochlea development / voltage-gated potassium channel activity / response to axon injury / response to mechanical stimulus / voltage-gated potassium channel complex / axon terminus / calyx of Held / potassium ion transmembrane transport / regulation of membrane potential / potassium ion transport / Schaffer collateral - CA1 synapse / memory / cellular response to hypoxia / postsynapse / 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 / : / HEXADECANE / : / Potassium channel subfamily K member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMondal, A. / Lee, H. / 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(S131C mutant) with ML335
Authors: Mondal, A. / Lee, H. / Minor, D.L.
History
DepositionSep 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 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

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)67,25327
Polymers63,1562
Non-polymers4,09825
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.213, 120.568, 128.613
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: 31577.910 Da / Num. of mol.: 2 / Fragment: residues 35-321
Mutation: S131C, as well as 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 , 6 types, 25 molecules

#2: 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
#3: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C10H22
#4: Chemical ChemComp-WUZ / N-[(2,4-dichlorophenyl)methyl]-4-[(3R)-3-methyl-2,5-dioxopyrrolidin-1-yl]benzamide


Mass: 391.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16Cl2N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34
#7: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd

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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: 4.27 Å3/Da / Density % sol: 71.17 %
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, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 3→43.36 Å / Num. obs: 21579 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.998 / Net I/σ(I): 6.5
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 1555 / CC1/2: 0.145

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→29.35 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 37.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2932 997 5.04 %
Rwork0.2734 --
obs0.2745 19787 91.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4280 0 256 0 4536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044620
X-RAY DIFFRACTIONf_angle_d0.7156212
X-RAY DIFFRACTIONf_dihedral_angle_d15.1871642
X-RAY DIFFRACTIONf_chiral_restr0.045715
X-RAY DIFFRACTIONf_plane_restr0.006736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.42661040.35242141X-RAY DIFFRACTION75
3.16-3.360.36181280.29732384X-RAY DIFFRACTION82
3.36-3.610.28861390.25992628X-RAY DIFFRACTION91
3.61-3.980.27781530.2382769X-RAY DIFFRACTION96
3.98-4.550.2971490.23022868X-RAY DIFFRACTION98
4.55-5.730.26821610.27732935X-RAY DIFFRACTION99
5.73-29.350.29371630.29023065X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 2.5095 Å / Origin y: -23.5342 Å / Origin z: -27.2587 Å
111213212223313233
T0.5166 Å2-0.0007 Å20.0151 Å2-0.6534 Å20.0854 Å2--0.454 Å2
L3.977 °2-0.2182 °20.9417 °2-3.3818 °2-0.6571 °2--4.5977 °2
S-0.0569 Å °0.4416 Å °-0.3946 Å °0.1314 Å °0.3606 Å °0.2176 Å °0.2308 Å °-0.4212 Å °-0.1933 Å °
Refinement TLS groupSelection details: all

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