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- PDB-3syo: Crystal structure of the G protein-gated inward rectifier K+ chan... -

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Basic information

Entry
Database: PDB / ID: 3syo
TitleCrystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (Kir3.2) in complex with sodium
ComponentsG protein-activated inward rectifier potassium channel 2
KeywordsMETAL TRANSPORT / ion channel / potassium channel / inward rectification / sodium binding / PIP2 binding / G protein binding
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 / 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 / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel C-terminal domain / Inward rectifier potassium channel, C-terminal / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Helix Hairpins - #70 / Immunoglobulin E-set ...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 / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel C-terminal domain / Inward rectifier potassium channel, C-terminal / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Helix Hairpins - #70 / Immunoglobulin E-set / Helix Hairpins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
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: 3.54 Å
AuthorsWhorton, M.R. / MacKinnon, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Crystal Structure of the Mammalian GIRK2 K(+) Channel and Gating Regulation by G Proteins, PIP(2), and Sodium.
Authors: Whorton, M.R. / Mackinnon, R.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release

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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)39,3208
Polymers39,0621
Non-polymers2587
Water0
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)157,27832
Polymers156,2484
Non-polymers1,03028
Water0
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 area27840 Å2
ΔGint-210 kcal/mol
Surface area49450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.737, 85.737, 178.602
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-501-

K

21A-502-

K

31A-503-

K

41A-504-

K

51A-505-

K

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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: 39061.957 Da / Num. of mol.: 1 / Fragment: UNP residues 52-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Girk2, Kcnj6, Kcnj7, W / Plasmid: pPICZ / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1163 / References: UniProt: P48542
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
Sequence detailsUNP P48542 S260T, I313M, AND M344L ARE NATURAL VARIANTS.

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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: 4.2 Å3/Da / Density % sol: 70.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM sodium citrate, pH 6.0, 1 M sodium chloride, 30-35% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2009
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.54→41.685 Å / Num. obs: 7975 / % possible obs: 92 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.158 / Χ2: 1.605 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.57-3.73.40.7296341.081176.8
3.7-3.854.60.5887311.175186.8
3.85-4.0270.6557671.065191.9
4.02-4.239.50.4618061.125196
4.23-4.59.50.2878281.483196.3
4.5-4.849.70.2178081.606194.9
4.84-5.339.40.188321.626196.6
5.33-6.19.40.1728401.581195.2
6.1-7.6890.128461.925195.1
7.68-41.6857.90.0588832.65190.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0110refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E4F
Resolution: 3.54→41.68 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.13 / SU B: 55.693 / SU ML: 0.404 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.58 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 566 7.1 %RANDOM
Rwork0.2604 ---
obs0.2613 7970 92.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 315.82 Å2 / Biso mean: 140.4722 Å2 / Biso min: 68.95 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.54→41.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 7 0 2399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222446
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9463331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2825306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14423.53599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23115387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.441511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211814
X-RAY DIFFRACTIONr_mcbond_it0.4481.51532
X-RAY DIFFRACTIONr_mcangle_it0.84122465
X-RAY DIFFRACTIONr_scbond_it0.853914
X-RAY DIFFRACTIONr_scangle_it1.5754.5866
LS refinement shellResolution: 3.544→3.635 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 31 -
Rwork0.301 409 -
all-440 -
obs--71.78 %
Refinement TLS params.Method: refined / Origin x: -9.6666 Å / Origin y: 30.9521 Å / Origin z: -36.7835 Å
111213212223313233
T0.2211 Å20.0025 Å2-0.0836 Å2-0.2329 Å2-0.0823 Å2--0.2223 Å2
L1.5125 °20.3341 °2-0.2975 °2-1.2541 °2-0.9845 °2--2.1424 °2
S-0.0622 Å °0.5383 Å °0.01 Å °-0.404 Å °-0.0029 Å °0.2196 Å °0.2286 Å °-0.1278 Å °0.0651 Å °

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