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- PDB-3spi: Inward rectifier potassium channel Kir2.2 in complex with PIP2 -

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Basic information

Entry
Database: PDB / ID: 3spi
TitleInward rectifier potassium channel Kir2.2 in complex with PIP2
ComponentsInward-rectifier K+ channel Kir2.2
KeywordsMETAL TRANSPORT / PIP / membrane protein / lipid / receptor
Function / homology
Function and homology information


Activation of G protein gated Potassium channels / Classical Kir channels / Phase 4 - resting membrane potential / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / monoatomic ion channel complex / potassium ion import across plasma membrane / potassium ion transport / protein homotetramerization ...Activation of G protein gated Potassium channels / Classical Kir channels / Phase 4 - resting membrane potential / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / monoatomic ion channel complex / potassium ion import across plasma membrane / potassium ion transport / protein homotetramerization / identical protein binding / membrane / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir2.2 / Potassium channel, inwardly rectifying, Kir, N-terminal / Inward rectifier potassium channel N-terminal / 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 ...Potassium channel, inwardly rectifying, Kir2.2 / Potassium channel, inwardly rectifying, Kir, N-terminal / Inward rectifier potassium channel N-terminal / 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 / Helix Hairpins - #70 / Helix Hairpins / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Chem-PIO / ATP-sensitive inward rectifier potassium channel 12 / ATP-sensitive inward rectifier potassium channel 12
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.307 Å
AuthorsHansen, S.B. / Tao, X. / MacKinnon, R.
CitationJournal: Nature / Year: 2011
Title: Structural basis of PIP(2) activation of the classical inward rectifier K(+) channel Kir2.2.
Authors: Hansen, S.B. / Tao, X. / Mackinnon, R.
History
DepositionJul 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inward-rectifier K+ channel Kir2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2656
Polymers39,3621
Non-polymers9035
Water00
1
A: Inward-rectifier K+ channel Kir2.2
hetero molecules

A: Inward-rectifier K+ channel Kir2.2
hetero molecules

A: Inward-rectifier K+ channel Kir2.2
hetero molecules

A: Inward-rectifier K+ channel Kir2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,05924
Polymers157,4474
Non-polymers3,61220
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area29230 Å2
ΔGint-167 kcal/mol
Surface area54840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.326, 83.326, 184.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-501-

K

21A-502-

K

31A-503-

K

41A-504-

K

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Components

#1: Protein Inward-rectifier K+ channel Kir2.2 / inward rectifier potassium channel 2.2


Mass: 39361.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: Kir2.2 / Production host: Pichia pastoris (fungus) / References: UniProt: D2YW45, UniProt: F1NHE9*PLUS
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H49O19P3
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.07 Å3/Da / Density % sol: 69.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10.62% PEG4000, 0.5 M potassium chloride, 0.05 M HEPES, pH 8.0, VAPOR DIFFUSION, HANGING 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: Aug 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 9392 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.5
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.0644 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.refine: 1.7_650)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SPH

3sph


Resolution: 3.307→36.357 Å / SU ML: 0.47 / σ(F): 0 / Phase error: 31.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2781 417 4.78 %
Rwork0.2354 --
obs0.2373 8723 92.41 %
all-9392 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.283 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-29.6168 Å20 Å20 Å2
2--29.6168 Å2-0 Å2
3---23.093 Å2
Refinement stepCycle: LAST / Resolution: 3.307→36.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 44 0 2703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122795
X-RAY DIFFRACTIONf_angle_d0.8353740
X-RAY DIFFRACTIONf_dihedral_angle_d14.81018
X-RAY DIFFRACTIONf_chiral_restr0.057424
X-RAY DIFFRACTIONf_plane_restr0.003470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3067-3.78470.37071300.32152512X-RAY DIFFRACTION84
3.7847-4.76670.22421500.21312827X-RAY DIFFRACTION95
4.7667-36.35950.28551370.2262967X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7285-0.32051.24981.95640.60381.25810.086-0.48850.19090.22890.18840.2989-0.5467-0.302600.61740.1322-0.02830.65530.01650.7219-49.5091-31.052654.5791
22.3241.13210.15011.91190.20591.9572-0.17330.13010.0853-0.13570.0309-0.2869-0.40740.4541-0.00050.5905-0.08630.04260.75780.03280.679-25.554-27.8112-0.2377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 78:186))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 187:372))

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