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- PDB-5um4: Crystal structure of the F255A mutant Kir3.1 cytoplasmic pore domain -

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Basic information

Entry
Database: PDB / ID: 5um4
TitleCrystal structure of the F255A mutant Kir3.1 cytoplasmic pore domain
ComponentsG protein-activated inward rectifier potassium channel 1
KeywordsTRANSPORT PROTEIN / inward-rectifier K(+) 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 speciesAnolis carolinensis (green anole)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsMeinke, G. / Bohm, A. / Noujaim, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: To Be Published
Title: Crystal structure of the F255A mutant Kir3.1 cytoplasmic pore domain
Authors: Meinke, G. / Bohm, A. / Noujaim, S.
History
DepositionJan 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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


Theoretical massNumber of molelcules
Total (without water)24,0461
Polymers24,0461
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.070, 80.070, 85.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

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


Mass: 24046.418 Da / Num. of mol.: 1 / Fragment: unp residues 41-63; unp residues 190-370 / Mutation: F255A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anolis carolinensis (green anole), (gene. exp.) Mus musculus (house mouse)
Gene: LOC100559481, Kcnj3, Girk1 / Production host: Escherichia coli (E. coli) / References: UniProt: H9GIV0, UniProt: P63250
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: The protein was concentrated to 10 mg/mL. Crystals grown by mixing equal amounts of protein and reservoir solution (25 mM Na/K phosphate pH 5.0, 40 mM NaCl, 35 % Peg 400), and allowed to ...Details: The protein was concentrated to 10 mg/mL. Crystals grown by mixing equal amounts of protein and reservoir solution (25 mM Na/K phosphate pH 5.0, 40 mM NaCl, 35 % Peg 400), and allowed to equilibrate over 1 ml of reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0003 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 1.987→85.04 Å / Num. all: 10030 / Num. obs: 10030 / % possible obs: 99.6 % / Redundancy: 12.5 % / Biso Wilson estimate: 61.61 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Rsym value: 0.064 / Net I/av σ(I): 7.5 / Net I/σ(I): 21.9 / Num. measured all: 125290
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.5-2.6413.20.5911.30.1690.6150.591100
2.64-2.813.20.3771.90.1080.3930.377100
2.8-2.9913.10.1973.70.0560.2050.197100
2.99-3.2312.90.1136.20.0330.1180.113100
3.23-3.5412.70.07490.0220.0770.074100
3.54-3.9512.30.055110.0160.0570.05599.6
3.95-4.5611.70.05210.30.0160.0540.05299.6
4.56-5.59110.05610.20.0170.0590.05699.9
5.59-7.9111.60.0415.40.0120.0420.04100
2.5-2.6410.10.0283.50.0090.030.02889.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.53 Å85.04 Å
Translation6.53 Å85.04 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.6.1phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N9P

1n9p


Resolution: 2.5→85.04 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 35.13
RfactorNum. reflection% reflection
Rfree0.2667 888 5.04 %
Rwork0.2241 --
obs0.2263 17623 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.35 Å2 / Biso mean: 67.2839 Å2 / Biso min: 39.22 Å2
Refinement stepCycle: final / Resolution: 2.5→85.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 0 27 1571
Biso mean---62.61 -
Num. residues----197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011581
X-RAY DIFFRACTIONf_angle_d1.1372138
X-RAY DIFFRACTIONf_chiral_restr0.06244
X-RAY DIFFRACTIONf_plane_restr0.006276
X-RAY DIFFRACTIONf_dihedral_angle_d3.2131320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5002-2.65680.51061420.37242823296597
2.6568-2.8620.34221360.33062747288395
2.862-3.150.3181540.27852687284193
3.15-3.60580.3031670.23852785295298
3.6058-4.54290.21611480.17982865301398
4.5429-85.08920.22981410.20482828296997

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