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- PDB-3auw: Cytoplasmic domain of inward rectifier potassium channel Kir3.2 i... -

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Basic information

Entry
Database: PDB / ID: 3auw
TitleCytoplasmic domain of inward rectifier potassium channel Kir3.2 in complex with cadmium
Components(Potassium inwardly-rectifying channel, subfamily J, member ...) x 2
KeywordsTRANSPORT PROTEIN / immunogloblin-like fold / 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 / presynaptic membrane / 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
: / ETHANOL / 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 / molecular replacement / Resolution: 3.56 Å
AuthorsInanobe, A. / Kurachi, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Inverse agonist-like action of cadmium on G-protein-gated inward-rectifier K(+) channels
Authors: Inanobe, A. / Matsuura, T. / Nakagawa, A. / Kurachi, Y.
History
DepositionFeb 17, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Refinement description / Category: software
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: Potassium inwardly-rectifying channel, subfamily J, member 6
C: Potassium inwardly-rectifying channel, subfamily J, member 6
D: Potassium inwardly-rectifying channel, subfamily J, member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,90010
Polymers47,5344
Non-polymers3666
Water724
1
A: Potassium inwardly-rectifying channel, subfamily J, member 6
B: Potassium inwardly-rectifying channel, subfamily J, member 6
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)95,79920
Polymers95,0688
Non-polymers73112
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
Buried area17640 Å2
ΔGint-55 kcal/mol
Surface area35520 Å2
MethodPISA
2
C: Potassium inwardly-rectifying channel, subfamily J, member 6
D: Potassium inwardly-rectifying channel, subfamily J, member 6
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)95,79920
Polymers95,0688
Non-polymers73112
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area17460 Å2
ΔGint-32 kcal/mol
Surface area35030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.808, 100.808, 105.812
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-1-

MG

21D-2-

MG

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Components

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Potassium inwardly-rectifying channel, subfamily J, member ... , 2 types, 4 molecules ACBD

#1: Protein/peptide Potassium inwardly-rectifying channel, subfamily J, member 6 / G protein-gated inward rectifier potassium channel Kir3.2


Mass: 3115.602 Da / Num. of mol.: 2 / Fragment: Cytoplasmic N-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnj6 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q0VB45, UniProt: P48542*PLUS
#2: Protein Potassium inwardly-rectifying channel, subfamily J, member 6 / G protein-gated inward rectifier potassium channel Kir3.2


Mass: 20651.393 Da / Num. of mol.: 2 / Fragment: Cytoplasmic C-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnj6 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q0VB45, UniProt: P48542*PLUS

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Non-polymers , 4 types, 10 molecules

#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EOH / ETHANOL / Ethanol


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


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 6, 2008
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.56→50 Å / Num. all: 27243 / Num. obs: 26865 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.206 / Net I/σ(I): 6.714

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.56→30 Å / Cor.coef. Fo:Fc: 0.835 / Cor.coef. Fo:Fc free: 0.76 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 98.167 / SU ML: 0.661 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.863 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3311 683 9.9 %RANDOM
Rwork0.2814 ---
obs0.2865 6884 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 78.11 Å2 / Biso mean: 34.1835 Å2 / Biso min: 22.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 3.56→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 10 4 3078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0223130
X-RAY DIFFRACTIONr_angle_refined_deg0.7631.9554232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3095380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85223.973146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46715552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4251520
X-RAY DIFFRACTIONr_chiral_restr0.0560.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212340
X-RAY DIFFRACTIONr_mcbond_it0.1711.51910
X-RAY DIFFRACTIONr_mcangle_it0.36123098
X-RAY DIFFRACTIONr_scbond_it0.59431220
X-RAY DIFFRACTIONr_scangle_it1.0684.51134
LS refinement shellResolution: 3.559→3.651 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 49 -
Rwork0.3 439 -
all-488 -
obs--98.99 %
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)
12.11212.546-2.000510.7794-1.00952.18560.1781-0.2543-0.27420.4664-0.3349-0.5125-0.01150.25590.15680.44290.1116-0.14490.3820.08780.2994-31.9905-20.0067-2.6673
21.06560.0363-0.41571.00960.03421.2691-0.0155-0.0051-0.0125-0.02590.0074-0.11710.04210.13730.0080.237-0.0031-0.03780.3028-0.01430.2319-29.52781.7992-15.3269
30.8921-1.43921.02022.8017-2.17312.5720.04880.0173-0.37660.00270.09020.26120.54230.0069-0.13910.53070.0144-0.08450.3499-0.09370.45431.696222.9997-50.1569
41.38810.0081-0.31850.6953-0.56431.1052-0.00980.0431-0.19450.0170.00930.07980.1264-0.09030.00050.2577-0.0451-0.04760.2628-0.00390.3002-15.796336.7932-37.7111
50.48130.484-0.43650.4918-0.44130.4012-0.00090.03220.0246-0.03160.0009-0.0246-0.01810.018500.4475-0.07490.30040.45290.29560.4733-25.202425.2029-26.3088
60.2210.06950.1920.07530.09020.1843-0.01750.03950.0251-0.002-0.00970.0343-0.02640.02680.02710.33290.01560.00690.3761-0.0530.3493-16.90235.7446-26.5593
71.72980.38470.34680.08630.07810.07090.11130.12-0.44840.0232-0.0051-0.08320.01550.032-0.10610.4067-0.07420.00180.05360.0890.7307-28.575433.1228-26.3161
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 71
2X-RAY DIFFRACTION2B204 - 378
3X-RAY DIFFRACTION3C55 - 71
4X-RAY DIFFRACTION4D204 - 378
5X-RAY DIFFRACTION5B1
6X-RAY DIFFRACTION5D2
7X-RAY DIFFRACTION6A1
8X-RAY DIFFRACTION6C2
9X-RAY DIFFRACTION7B382
10X-RAY DIFFRACTION7D382

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