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- PDB-3atf: Crystal Structure of the Kir3.2 Cytoplasmic Domain (Na+-free crys... -

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Basic information

Entry
Database: PDB / ID: 3atf
TitleCrystal Structure of the Kir3.2 Cytoplasmic Domain (Na+-free crystal soaked in 200 mM Cesium chloride)
ComponentsPotassium inwardly-rectifying channel, subfamily J, member 6
KeywordsTRANSPORT PROTEIN / Cytoplasmic assembly / beta-barrel / ion transport / G protein beta-gamma subunits
Function / homology
Function and homology information


G-protein activated inward rectifier potassium channel activity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / inward rectifier potassium channel activity / neuronal cell body membrane / parallel fiber to Purkinje cell synapse / potassium ion import across plasma membrane / G-protein alpha-subunit binding / regulation of ion transmembrane transport / integral component of presynaptic membrane ...G-protein activated inward rectifier potassium channel activity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / inward rectifier potassium channel activity / neuronal cell body membrane / parallel fiber to Purkinje cell synapse / potassium ion import across plasma membrane / G-protein alpha-subunit binding / regulation of ion transmembrane transport / integral component of presynaptic membrane / axon / dendrite / cell surface / integral component of membrane / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel, inwardly rectifying, Kir3.2 / 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 / Immunoglobulin E-set / Immunoglobulin-like ...Potassium channel, inwardly rectifying, Kir3.2 / 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 / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
G protein-activated inward rectifier potassium channel 2 / : / ETHANOL / G protein-activated inward rectifier potassium channel 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsInanobe, A. / Kurachi, Y.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Interactions of cations with the cytoplasmic pores of inward rectifier K(+) channels in the closed state
Authors: Inanobe, A. / Nakagawa, A. / Kurachi, Y.
History
DepositionDec 28, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium inwardly-rectifying channel, subfamily J, member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1316
Polymers23,7491
Non-polymers3825
Water23413
1
A: Potassium inwardly-rectifying channel, subfamily J, member 6
hetero molecules

A: Potassium inwardly-rectifying channel, subfamily J, member 6
hetero molecules

A: Potassium inwardly-rectifying channel, subfamily J, member 6
hetero molecules

A: Potassium inwardly-rectifying channel, subfamily J, member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,52524
Polymers94,9964
Non-polymers1,52920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area11480 Å2
ΔGint-10 kcal/mol
Surface area34430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.732, 81.732, 172.125
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-382-

MG

21A-8-

HOH

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Components

#1: Protein Potassium inwardly-rectifying channel, subfamily J, member 6 / G protein-activated inward rectifier potassium channel 2


Mass: 23748.988 Da / Num. of mol.: 1 / Fragment: RESIDUES 53-74, 200-381
Source method: isolated from a genetically manipulated source
Details: CYTOPLASMIC N- AND C-TERMINI (RESIDUES 53-74 AND 200-381, RESPECTIVELY) OF G-PROTEIN-GATED INWARD RECTIFIER POTASSIUM CHANNEL KIR3.2 ARE CONCATENATED DIRECTLY.
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSSETA2 (DE3) / References: UniProt: Q0VB45, UniProt: P48542*PLUS
#2: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.35 %
Crystal growTemperature: 277 K / Method: hanging drop / pH: 8 / Details: Ethanol, pH 8.0, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.6 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 10, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 338695 / Num. obs: 338691 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 52.3 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 48.4
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 31.1 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 5.88 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→47.98 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.863 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 16.586 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.281 490 7.6 %RANDOM
Rwork0.2231 ---
obs0.2274 6475 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 161.76 Å2 / Biso mean: 44.7397 Å2 / Biso min: 10.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.95→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 9 13 1568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221587
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9562144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58523.86775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30115283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1271511
X-RAY DIFFRACTIONr_chiral_restr0.080.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211187
X-RAY DIFFRACTIONr_mcbond_it0.6541.5964
X-RAY DIFFRACTIONr_mcangle_it1.25521565
X-RAY DIFFRACTIONr_scbond_it1.4713623
X-RAY DIFFRACTIONr_scangle_it2.6214.5578
LS refinement shellResolution: 2.952→3.029 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 44 -
Rwork0.326 413 -
all-457 -
obs--97.86 %

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