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- PDB-2e4f: Crystal Structure of the Cytoplasmic Domain of G-Protein-Gated In... -

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Basic information

Entry
Database: PDB / ID: 2e4f
TitleCrystal Structure of the Cytoplasmic Domain of G-Protein-Gated Inward Rectifier Potassium Channel Kir3.2
ComponentsG protein-activated inward rectifier potassium channel 2
KeywordsTRANSPORT PROTEIN / cytoplasmic assembly / ion channel / beta-barrel
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
G protein-activated inward rectifier potassium channel 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsInanobe, A. / Kurachi, Y.
CitationJournal: CHANNELS / Year: 2007
Title: Structural Diversity in the Cytoplasmic Region of G Protein-Gated Inward Rectifier K+ Channels
Authors: Inanobe, A. / Matsuura, T. / Nakagawa, A. / Kurachi, Y.
History
DepositionDec 6, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE THR A 260 is from ISOFORM GIRK2D, MET 313 and LEU 344 are from VARIANT.

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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


Theoretical massNumber of molelcules
Total (without water)23,7351
Polymers23,7351
Non-polymers00
Water1,964109
1
A: G protein-activated inward rectifier potassium channel 2

A: G protein-activated inward rectifier potassium channel 2

A: G protein-activated inward rectifier potassium channel 2

A: G protein-activated inward rectifier potassium channel 2


Theoretical massNumber of molelcules
Total (without water)94,9404
Polymers94,9404
Non-polymers00
Water724
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 area10230 Å2
ΔGint-24 kcal/mol
Surface area35060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.173, 77.173, 87.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Detailstetramer individual symmetry operations for each subunit are following: X,Y.Z -X,1-Y,Z -1/2+Y,1/2-X,Z 1/2-Y,1/2+X,Z

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Components

#1: Protein G protein-activated inward rectifier potassium channel 2 / GIRK2 / Potassium channel / inwardly rectifying subfamily J member 6 / Inward rectifier K+ / channel Kir3.2


Mass: 23734.961 Da / Num. of mol.: 1 / Fragment: residues 53-74, 200-381
Source method: isolated from a genetically manipulated source
Details: An amino terminus (amino residues: 53-74) of longst isoform of mouse Kir3.2 (Kir3.2c) was directly concatenated to a carboxyl terminus (amino residues: 200-381) and subcloned into NdeI and XhoI sites of pET28A.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnj6 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta2 (DE3) / References: UniProt: P48542
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.74 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES-NaOH, 0.2M MgCl2, 30%(v/v) iso-propanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Dec 6, 2005
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.302→46.274 Å / Num. all: 12226 / Num. obs: 12201 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 15.5
Reflection shellResolution: 2.302→2.38 Å / Redundancy: 9 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 4.93 / Num. unique all: 1181 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N9P

1n9p


Resolution: 2.302→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 1190 -RANDOM
Rwork0.2438 ---
all-12081 --
obs-11612 96.1 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.253 Å20 Å20 Å2
2---2.253 Å20 Å2
3---4.507 Å2
Refinement stepCycle: LAST / Resolution: 2.302→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1485 0 0 109 1594
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.45
X-RAY DIFFRACTIONc_improper_angle_d0.912
X-RAY DIFFRACTIONc_dihedral_angle_d26.254

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