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- PDB-3ukm: Crystal structure of the human two pore domain potassium ion chan... -

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Basic information

Entry
Database: PDB / ID: 3ukm
TitleCrystal structure of the human two pore domain potassium ion channel K2P1 (TWIK-1)
ComponentsPotassium channel subfamily K member 1
KeywordsMEMBRANE PROTEIN / potassium channel / eukaryotic / two-pore domain potassium channel / K2P channel / membrane
Function / homology
Function and homology information


Tandem of pore domain in a weak inwardly rectifying K+ channels (TWIK) / inward rectifier potassium channel complex / Phase 4 - resting membrane potential / potassium channel complex / regulation of resting membrane potential / stabilization of membrane potential / cardiac conduction / potassium ion leak channel activity / inward rectifier potassium channel activity / sodium channel activity ...Tandem of pore domain in a weak inwardly rectifying K+ channels (TWIK) / inward rectifier potassium channel complex / Phase 4 - resting membrane potential / potassium channel complex / regulation of resting membrane potential / stabilization of membrane potential / cardiac conduction / potassium ion leak channel activity / inward rectifier potassium channel activity / sodium channel activity / potassium channel activity / plasma membrane => GO:0005886 / sodium ion transmembrane transport / potassium ion transmembrane transport / voltage-gated potassium channel complex / synaptic membrane / brush border membrane / response to nicotine / potassium ion transport / recycling endosome / perikaryon / membrane => GO:0016020 / apical plasma membrane / intracellular membrane-bounded organelle / dendrite / identical protein binding / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TWIK-1 / Two pore domain potassium channel, TWIK family / Two pore domain potassium channel, TASK family / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / UNDECANE / Potassium channel subfamily K member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 3.4 Å
AuthorsLong, S.B. / Miller, A.N.
CitationJournal: Science / Year: 2012
Title: Crystal structure of the human two-pore domain potassium channel K2P1.
Authors: Miller, A.N. / Long, S.B.
History
DepositionNov 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel subfamily K member 1
B: Potassium channel subfamily K member 1
C: Potassium channel subfamily K member 1
D: Potassium channel subfamily K member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,66018
Polymers127,6444
Non-polymers1,01614
Water1448
1
A: Potassium channel subfamily K member 1
B: Potassium channel subfamily K member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3309
Polymers63,8222
Non-polymers5087
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-56 kcal/mol
Surface area23410 Å2
MethodPISA
2
C: Potassium channel subfamily K member 1
D: Potassium channel subfamily K member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3309
Polymers63,8222
Non-polymers5087
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-56 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.080, 123.171, 119.305
Angle α, β, γ (deg.)90.00, 94.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Potassium channel subfamily K member 1 / Inward rectifying potassium channel protein TWIK-1 / Potassium channel KCNO1


Mass: 31910.986 Da / Num. of mol.: 4 / Fragment: UNP residues 19-288 / Mutation: W21T, C22M, N95Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HOHO1, K2P1 (TWIK-1), KCNK1, KCNO1, TWIK1 / Production host: Komagataella pastoris (fungus) / References: UniProt: O00180
#2: Chemical
ChemComp-UND / UNDECANE / LIPID FRAGMENT


Mass: 156.308 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H24
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 4.71 Å3/Da / Density % sol: 73.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% Peg 400, 150 mM KCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2011
RadiationMonochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 32855 / Num. obs: 32855 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Rsym value: 0.057 / Net I/σ(I): 38.5
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 12 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1628 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
CNS1.3refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 3.4→19.91 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 153625.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1479 5.1 %RANDOM
Rwork0.273 ---
obs0.273 29136 89.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 131.864 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 185.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.96 Å20 Å216.17 Å2
2---19.95 Å20 Å2
3---12.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.66 Å0.63 Å
Luzzati d res low-5 Å
Luzzati sigma a1.01 Å1.13 Å
Refinement stepCycle: LAST / Resolution: 3.4→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7544 0 54 8 7606
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.22
X-RAY DIFFRACTIONc_mcangle_it6.792.5
X-RAY DIFFRACTIONc_scbond_it7.473
X-RAY DIFFRACTIONc_scangle_it10.254
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.4→3.52 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.467 147 5.5 %
Rwork0.473 2549 -
obs-2549 83.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6POpgb.

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