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- PDB-3spc: Inward rectifier potassium channel Kir2.2 in complex with dioctan... -

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Basic information

Entry
Database: PDB / ID: 3spc
TitleInward rectifier potassium channel Kir2.2 in complex with dioctanoylglycerol pyrophosphate (DGPP)
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 / regulation of monoatomic ion transmembrane transport / inward rectifier potassium channel activity / potassium ion import across plasma membrane / monoatomic ion channel complex / T-tubule / potassium ion transport ...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 / regulation of monoatomic ion transmembrane transport / inward rectifier potassium channel activity / potassium ion import across plasma membrane / monoatomic ion channel complex / T-tubule / 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-P8P / 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: 2.454 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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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)40,1018
Polymers39,3621
Non-polymers7397
Water1,58588
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)160,40332
Polymers157,4474
Non-polymers2,95628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area27640 Å2
ΔGint-173 kcal/mol
Surface area57030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.904, 82.904, 191.159
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

51A-508-

K

61A-510-

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.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-P8P / (2R)-3-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}propane-1,2-diyl dioctanoate / dioctanoylglycerol pyrophosphate


Mass: 504.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H38O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.17 Å3/Da / Density % sol: 70.52 %
Crystal growMethod: hanging drop, vapor diffusion / pH: 7
Details: 6.2% PEG400, 0.5 M potassium chloride, 0.1 M HEPES, pH 7.0, HANGING DROP, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2011
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→16 Å / Num. obs: 23341 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Rsym value: 0.146 / Net I/σ(I): 11.7
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.2 / % 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 3JYC

3jyc


Resolution: 2.454→15.657 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 1120 5.05 %R-Free values were generated from PDB entry 3JYC and extended to higher resolution frames.
Rwork0.1929 ---
obs0.1944 22164 94.58 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.91 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.7079 Å20 Å2-0 Å2
2--4.7079 Å20 Å2
3----9.4158 Å2
Refinement stepCycle: LAST / Resolution: 2.454→15.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 34 88 2727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112729
X-RAY DIFFRACTIONf_angle_d0.8823639
X-RAY DIFFRACTIONf_dihedral_angle_d14.018983
X-RAY DIFFRACTIONf_chiral_restr0.064412
X-RAY DIFFRACTIONf_plane_restr0.003459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4542-2.56540.36791290.28572360X-RAY DIFFRACTION85
2.5654-2.70.2781400.24512471X-RAY DIFFRACTION89
2.7-2.86820.2521460.21822557X-RAY DIFFRACTION92
2.8682-3.08810.23311450.21032638X-RAY DIFFRACTION95
3.0881-3.3960.25661420.19482731X-RAY DIFFRACTION98
3.396-3.88090.19591480.18232763X-RAY DIFFRACTION100
3.8809-4.8650.19351480.1612797X-RAY DIFFRACTION100
4.865-15.65720.22791220.20242727X-RAY DIFFRACTION97
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)
13.6881-1.1765-1.32543.4751-0.79631.2424-0.0213-0.3494-0.17220.41050.0303-0.30330.39430.67830.00030.63670.0857-0.08140.6430.0130.603610.673-7.700341.4676
22.29990.26580.36012.89930.08862.52170.03110.01610.2993-0.0917-0.119-0.4487-0.35890.3577-0.00010.6795-0.1234-0.02370.67230.02970.690515.41114.738996.6326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 69:187))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 42:62) or (resseq 193:372))

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