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- PDB-8ue9: Structure of TREK-1CG*:CAT335 -

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Basic information

Entry
Database: PDB / ID: 8ue9
TitleStructure of TREK-1CG*:CAT335
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
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 / : / : / 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 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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)67,70024
Polymers63,1562
Non-polymers4,54422
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.069, 119.776, 129.708
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, 23 molecules

#2: Chemical
ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C16H34
#3: Chemical ChemComp-WUU / N-[(2,4-dichlorophenyl)methyl]-4-(2,5-dioxopyrrolidin-1-yl)benzamide


Mass: 377.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H14Cl2N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#7: Water ChemComp-HOH / 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 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: 4.24 Å3/Da / Density % sol: 70.96 %
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: Jul 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 3→46.62 Å / Num. obs: 21576 / % possible obs: 99.85 % / Redundancy: 19 % / CC1/2: 0.993 / Net I/σ(I): 6.8
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 2112 / CC1/2: 0.207

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→46.62 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 31.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.306 1041 4.83 %
Rwork0.2679 --
obs0.2696 21555 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 302 1 4643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024732
X-RAY DIFFRACTIONf_angle_d0.5666344
X-RAY DIFFRACTIONf_dihedral_angle_d15.97792
X-RAY DIFFRACTIONf_chiral_restr0.041718
X-RAY DIFFRACTIONf_plane_restr0.003747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.37381540.32382877X-RAY DIFFRACTION100
3.16-3.360.32031600.27382860X-RAY DIFFRACTION100
3.36-3.610.32421550.26952870X-RAY DIFFRACTION100
3.62-3.980.29071550.22312888X-RAY DIFFRACTION100
3.98-4.550.27531400.23552932X-RAY DIFFRACTION100
4.55-5.740.32981390.26052978X-RAY DIFFRACTION100
5.74-46.620.29951380.28783109X-RAY DIFFRACTION100
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)
18.0923.60325.77979.14192.36422.48770.7108-0.2562-1.94950.67630.1570.16411.0513-0.2844-0.83281.26670.037-0.11571.08210.2021.02322.6824-37.9093-17.3629
28.764-2.4195-2.94556.6099-1.35326.197-0.24420.26070.02330.90310.4575-0.1931-0.3277-1.2765-0.04640.75740.0552-0.05711.24350.24590.6804-3.0518-13.9022-31.8672
32.6378-0.0681-0.64.5564-0.55673.81150.18020.1741-0.44810.9424-0.02670.8955-0.4257-1.1741-0.01370.96380.28230.19871.34350.38060.6434-4.633-11.4486-16.0133
45.1985-4.85230.32771.917-0.945.5530.5784-0.4654-0.34750.70480.1680.00730.0432-0.2317-0.68250.93530.05370.0950.4180.23910.92577.4869-12.3146-15.5628
56.59012.7079-1.23057.05-2.18114.73510.06760.6596-0.78990.74810.57561.85560.6978-1.2606-0.74261.1337-0.0954-0.02881.66610.27511.3911-13.5803-29.6139-34.2426
64.9713-0.12323.36443.4934-0.58588.14490.12970.572-1.3096-0.22150.1289-0.59830.55041.18850.11320.73350.10590.07360.8996-0.06891.08712.7102-28.62-31.1578
74.5895-3.28292.58917.6087-3.89116.8152-0.47940.71940.4618-0.51880.1351-1.5199-0.8116-0.0640.31640.96930.07480.13861.1266-0.03740.9778.8417-14.991-43.5408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 110 )
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 199 )
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 259 )
4X-RAY DIFFRACTION4chain 'A' and (resid 260 through 321 )
5X-RAY DIFFRACTION5chain 'B' and (resid 35 through 112 )
6X-RAY DIFFRACTION6chain 'B' and (resid 113 through 269 )
7X-RAY DIFFRACTION7chain 'B' and (resid 270 through 316 )

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