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- PDB-3vsq: Crystal Structure of the Cytoplasmic Domain of G-Protein-Gated In... -

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Basic information

Entry
Database: PDB / ID: 3vsq
TitleCrystal Structure of the Cytoplasmic Domain of G-Protein-Gated Inward Rectifier Potassium Channel Kir3.2 E236R Mutant in the presence of ethanol
ComponentsG protein-activated inward rectifier potassium channel 2
KeywordsTRANSPORT PROTEIN / immunoglobulin-like fold
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
BETA-MERCAPTOETHANOL / 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: 2 Å
AuthorsInanobe, A. / Kurachi, Y.
CitationJournal: To be Published
Title: Coupling of G Protein Binding to Channel Gating in Mammalian Inward Rectifier K+ channels
Authors: Inanobe, A. / Kurachi, Y.
History
DepositionMay 2, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 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: G protein-activated inward rectifier potassium channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9584
Polymers23,7771
Non-polymers1813
Water1,51384
1
A: G protein-activated inward rectifier potassium channel 2
hetero molecules

A: G protein-activated inward rectifier potassium channel 2
hetero molecules

A: G protein-activated inward rectifier potassium channel 2
hetero molecules

A: G protein-activated inward rectifier potassium channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,83116
Polymers95,1084
Non-polymers72212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area13990 Å2
ΔGint-6 kcal/mol
Surface area34590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.863, 85.863, 73.046
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
11A-403-

MG

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Components

#1: Protein G protein-activated inward rectifier potassium channel 2 / GIRK-2 / Inward rectifier K(+) channel Kir3.2 / Potassium channel / inwardly rectifying subfamily J member 6


Mass: 23777.068 Da / Num. of mol.: 1 / Fragment: UNP residues 53-74, 200-381 / Mutation: E236R
Source method: isolated from a genetically manipulated source
Details: a concatemer of cytoplasmic N- and C-termini of G-Protein-Gated Inward Rectifier Potassium Channel Kir3.2
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnj6 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q8C4T8, UniProt: P48542*PLUS
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 56.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15%(v/v) ethanol, 0.1M HEPE-NaOH, 0.2M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.5 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jun 25, 2011
RadiationMonochromator: a double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 516819 / Num. obs: 516819 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 27.3 % / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 25.515
Reflection shellResolution: 2→2.07 Å / Redundancy: 27.2 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 6.189 / Rsym value: 0.801 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.053 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 967 5.1 %RANDOM
Rwork0.2163 ---
all0.2184 18913 --
obs0.2163 18813 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.53 Å2 / Biso mean: 42.8148 Å2 / Biso min: 27.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 9 84 1669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221634
X-RAY DIFFRACTIONr_angle_refined_deg1.0571.9562207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.855201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60423.5978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73615295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7511513
X-RAY DIFFRACTIONr_chiral_restr0.0730.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211221
X-RAY DIFFRACTIONr_mcbond_it0.7191.5987
X-RAY DIFFRACTIONr_mcangle_it1.34621603
X-RAY DIFFRACTIONr_scbond_it1.6963647
X-RAY DIFFRACTIONr_scangle_it2.9544.5601
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 88 -
Rwork0.272 1274 -
all-1362 -
obs--98.91 %

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