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- PDB-1n9p: Crystal Structure of the Cytoplasmic Domain of G-protein Activate... -

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Basic information

Entry
Database: PDB / ID: 1n9p
TitleCrystal Structure of the Cytoplasmic Domain of G-protein Activated Inward Rectifier Potassium Channel 1
ComponentsG protein-activated inward rectifier potassium channel 1
KeywordsMETAL TRANSPORT / BETA BARREL / CYTOPLASMIC DOMAIN / G PROTEIN / INWARD RECTIFIER / POTASSIUM CHANNEL
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 / potassium ion import across plasma membrane / voltage-gated potassium channel complex ...: / 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 / potassium ion import across plasma membrane / voltage-gated potassium channel complex / response to electrical stimulus / T-tubule / presynaptic membrane / external side of plasma membrane / cell surface / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir3.1 / 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, Kir3.1 / 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 1 / G protein-activated inward rectifier potassium channel 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsNishida, M. / MacKinnon, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Structural Basis of Inward Rectification: Cytoplasmic Pore of the G Protein-Gated Inward Rectifier GIRK1 at 1.8 A Resolution
Authors: Nishida, M. / MacKinnon, R.
History
DepositionNov 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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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 1


Theoretical massNumber of molelcules
Total (without water)23,9491
Polymers23,9491
Non-polymers00
Water2,522140
1
A: G protein-activated inward rectifier potassium channel 1

A: G protein-activated inward rectifier potassium channel 1

A: G protein-activated inward rectifier potassium channel 1

A: G protein-activated inward rectifier potassium channel 1


Theoretical massNumber of molelcules
Total (without water)95,7964
Polymers95,7964
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 area10360 Å2
ΔGint-9 kcal/mol
Surface area36540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.02, 76.02, 86.11
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-463-

HOH

21A-500-

HOH

DetailsThe biological assembly is a tetramer generated from the subunit in the asymmetric unit by the operations: x,y,z and -y+1/2,x+1/2,z and -x,-y+1,z and y-1/2,-x+1/2,z.

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Components

#1: Protein G protein-activated inward rectifier potassium channel 1 / GIRK1 / Potassium channel / inwardly rectifying / subfamily J / member 3 / Inward rectifier K+ ...GIRK1 / Potassium channel / inwardly rectifying / subfamily J / member 3 / Inward rectifier K+ channel Kir3.1 / KGA / KGB1


Mass: 23949.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: GIRK1 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P63250, UniProt: P35562
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.57 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: DTT, HEPES, magnesium acetate, PEG 400, sodium chloride, Tris-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
250 mMmagnesium acetate1reservoir
350 mMHEPES1reservoirpH7.0
455 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9792, 0.9790, 0.9640
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 11, 2002
RadiationMonochromator: SILICON / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.9791
30.9641
ReflectionResolution: 1.8→30 Å / Num. obs: 23971 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 19.1 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.057 / Net I/σ(I): 20.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 12.9 / Num. unique all: 2293 / Rsym value: 0.174 / % possible all: 96.6
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.174

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Methionine was replaced by selenomethionine through refinement and anomalous signal of selenium that was based on the experimental value was incorporated. Bijvoet pairs were treated as ...Details: Methionine was replaced by selenomethionine through refinement and anomalous signal of selenium that was based on the experimental value was incorporated. Bijvoet pairs were treated as separate reflections. No test flag was used in the final cycle of refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2237 5 %RANDOM
Rwork0.231 ---
all0.232 44247 --
obs0.232 43936 98.8 %-
Solvent computationBsol: 56.37 Å2 / ksol: 0.5 e/Å3
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 0 140 1725
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.357
X-RAY DIFFRACTIONc_dihedral_angle_d26.59
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 1.8→1.86 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.319 215 4.8 %
Rwork0.258 4054 -
obs-5336 95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.59
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.15

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