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- PDB-3k6n: Crystal structure of the S225E mutant Kir3.1 cytoplasmic pore domain -

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Basic information

Entry
Database: PDB / ID: 3k6n
TitleCrystal structure of the S225E mutant Kir3.1 cytoplasmic pore domain
ComponentsG protein-activated inward rectifier potassium channel 1
KeywordsMETAL TRANSPORT / BETA BARREL / CYTOPLASMIC DOMAIN / G PROTEIN / INWARD RECTIFIER / POTASSIUM CHANNEL / Ion transport / Ionic channel / Transmembrane
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 / response to electrical stimulus ...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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsXu, Y. / Shin, H.G. / Szep, S. / Lu, Z.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Physical determinants of strong voltage sensitivity of K(+) channel block.
Authors: Xu, Y. / Shin, H.G. / Szep, S. / Lu, Z.
History
DepositionOct 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7316
Polymers23,6161
Non-polymers1155
Water3,243180
1
A: G protein-activated inward rectifier potassium channel 1
hetero molecules

A: G protein-activated inward rectifier potassium channel 1
hetero molecules

A: G protein-activated inward rectifier potassium channel 1
hetero molecules

A: G protein-activated inward rectifier potassium channel 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,92324
Polymers94,4644
Non-polymers46020
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 area10370 Å2
ΔGint-40 kcal/mol
Surface area31830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.455, 77.455, 86.723
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-7-

NA

21A-8-

NA

31A-9-

NA

41A-10-

NA

51A-11-

NA

61A-507-

HOH

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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(+) channel Kir3.1


Mass: 23615.916 Da / Num. of mol.: 1 / Fragment: cytoplasmic domain / Mutation: S225E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Girk1, Kcnj3 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63250
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: sodium citrate, ammonium acetate, barium choride, MPD, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 16, 2004
RadiationMonochromator: Double silicon(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 18465 / Num. obs: 16877 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 11.2 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Χ2: 1.069 / Net I/σ(I): 39.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 7.8 / Num. unique all: 1788 / Rsym value: 0.35 / Χ2: 1.077 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.499 / Cor.coef. Fo:Fc: 0.488 / Cor.coef. Io to Ic: 0.421
Highest resolutionLowest resolution
Rotation3 Å40 Å
Translation3 Å30 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1N9P

1n9p


Resolution: 2→40 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.706 / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 844 -RANDOM
Rwork0.254 ---
all-18465 --
obs-16749 90.7 %-
Displacement parametersBiso max: 90.87 Å2 / Biso mean: 47.45 Å2 / Biso min: 23.21 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 5 180 1571
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.22

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