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

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Basic information

Entry
Database: PDB / ID: 3ata
TitleCrystal Structure of the Kir3.2 Cytoplasmic Domain (Na+-free crystal soaked in 10 mM barium chloride and 10 mM Spermine)
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 / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / monoatomic ion channel complex / neuronal cell body membrane / potassium ion import across plasma 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 / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / monoatomic ion channel complex / neuronal cell body membrane / potassium ion import across plasma membrane / potassium channel activity / G-protein alpha-subunit binding / negative regulation of insulin secretion / presynapse / presynaptic membrane / postsynapse / axon / dendrite / cell surface / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir3.2 / G protein-activated inward rectifier potassium channel 1 / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / Immunoglobulin E-set / Immunoglobulin-like ...Potassium channel, inwardly rectifying, Kir3.2 / G protein-activated inward rectifier potassium channel 1 / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / G protein-activated inward rectifier potassium channel 2 / G protein-activated inward rectifier potassium channel 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 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
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)23,8862
Polymers23,7491
Non-polymers1371
Water00
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)95,5458
Polymers94,9964
Non-polymers5494
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area12080 Å2
ΔGint-14 kcal/mol
Surface area34390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.691, 81.691, 172.429
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-1-

BA

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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-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba

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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: 59.38 %
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: Jun 2, 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: 3.49→50 Å / Num. all: 104396 / Num. obs: 104393 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 26.1 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 23.5
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 17.9 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 5.25 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.49→47.99 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.866 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 31.827 / SU ML: 0.495 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.697 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2802 562 14.1 %RANDOM
Rwork0.2212 ---
obs0.2295 3998 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 124.64 Å2 / Biso mean: 83.5237 Å2 / Biso min: 67.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 3.49→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1568 0 1 0 1569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221605
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.9562172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.795196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81823.94776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13915287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3111511
X-RAY DIFFRACTIONr_chiral_restr0.0720.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211203
X-RAY DIFFRACTIONr_mcbond_it0.4431.5977
X-RAY DIFFRACTIONr_mcangle_it0.82121587
X-RAY DIFFRACTIONr_scbond_it0.763628
X-RAY DIFFRACTIONr_scangle_it1.3824.5584
LS refinement shellResolution: 3.486→3.576 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 41 -
Rwork0.276 242 -
all-283 -
obs--95.61 %

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