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- PDB-3sph: Inward rectifier potassium channel Kir2.2 I223L mutant in complex... -

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Basic information

Entry
Database: PDB / ID: 3sph
TitleInward rectifier potassium channel Kir2.2 I223L mutant in complex with PIP2
ComponentsInward-rectifier K+ channel Kir2.2
KeywordsMETAL TRANSPORT / PIP / membrane protein / lipid / receptor
Function / homology
Function and homology information


inward rectifier potassium channel activity / potassium ion import across plasma membrane / intrinsic component of membrane / regulation of ion transmembrane transport / potassium ion transport / protein homotetramerization / integral component of membrane / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir2.2 / Inward rectifier potassium channel N-terminal / Potassium channel, inwardly rectifying, Kir, N-terminal / G protein-activated inward rectifier potassium channel 1 / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel C-terminal domain / Inward rectifier potassium channel, C-terminal / Potassium channel, inwardly rectifying, Kir / Potassium channel, inwardly rectifying, Kir, cytoplasmic ...Potassium channel, inwardly rectifying, Kir2.2 / Inward rectifier potassium channel N-terminal / Potassium channel, inwardly rectifying, Kir, N-terminal / G protein-activated inward rectifier potassium channel 1 / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel C-terminal domain / Inward rectifier potassium channel, C-terminal / Potassium channel, inwardly rectifying, Kir / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Helix Hairpins - #70 / Immunoglobulin E-set / Helix Hairpins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ATP-sensitive inward rectifier potassium channel 12 / : / Chem-PIO / ATP-sensitive inward rectifier potassium channel 12
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å
AuthorsHansen, S.B. / Tao, X. / MacKinnon, R.
CitationJournal: Nature / Year: 2011
Title: Structural basis of PIP(2) activation of the classical inward rectifier K(+) channel Kir2.2.
Authors: Hansen, S.B. / Tao, X. / Mackinnon, R.
History
DepositionJul 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inward-rectifier K+ channel Kir2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2656
Polymers39,3621
Non-polymers9035
Water0
1
A: Inward-rectifier K+ channel Kir2.2
hetero molecules

A: Inward-rectifier K+ channel Kir2.2
hetero molecules

A: Inward-rectifier K+ channel Kir2.2
hetero molecules

A: Inward-rectifier K+ channel Kir2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,05924
Polymers157,4474
Non-polymers3,61220
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area29720 Å2
ΔGint-154 kcal/mol
Surface area54730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.725, 82.725, 185.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-501-

K

21A-502-

K

31A-503-

K

41A-504-

K

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Components

#1: Protein Inward-rectifier K+ channel Kir2.2 / inward rectifier potassium channel 2.2


Mass: 39361.723 Da / Num. of mol.: 1 / Mutation: I223L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: Kir2.2 / Production host: Pichia pastoris (fungus) / References: UniProt: D2YW45, UniProt: F1NHE9*PLUS
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H49O19P3

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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: 4.02 Å3/Da / Density % sol: 69.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12.1% PEG400, 0.5 M potassium chloride, 0.05 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2010
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 12263 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 27.4
Reflection shellResolution: 3→3.1 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.7 / % possible all: 89.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.refine: 1.7_650)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SPG
Resolution: 3.003→36.303 Å / SU ML: 0.48 / σ(F): 0 / Phase error: 29.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 553 4.75 %
Rwork0.2168 --
obs0.2186 11630 93.57 %
all-17165 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.781 Å2 / ksol: 0.258 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--21.8367 Å2-0 Å2-0 Å2
2---21.8367 Å20 Å2
3----10.3105 Å2
Refinement stepCycle: LAST / Resolution: 3.003→36.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2665 0 44 0 2709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122801
X-RAY DIFFRACTIONf_angle_d0.9773747
X-RAY DIFFRACTIONf_dihedral_angle_d15.321023
X-RAY DIFFRACTIONf_chiral_restr0.062424
X-RAY DIFFRACTIONf_plane_restr0.003471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0032-3.30520.36041290.30932508X-RAY DIFFRACTION85
3.3052-3.78310.25831360.23232790X-RAY DIFFRACTION95
3.7831-4.76460.22551450.17042851X-RAY DIFFRACTION97
4.7646-36.30570.24891430.22272928X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.2768-0.5081-0.90992.2378-1.01771.06580.07940.0104-0.4044-0.23180.0896-0.19840.36020.69940.00040.6990.0895-0.01940.79780.08130.8136-30.4716-48.599-51.9962
22.65020.53441.23212.7714-0.5243.57890.0695-0.00970.1766-0.0394-0.1588-0.3258-0.40330.42890.00010.8168-0.1448-0.0030.7273-0.00630.8709-25.9251-27.6591-1.5176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 70:188))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 189:372)) or ((resseq 41:69))

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