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- PDB-3syq: Crystal structure of the G protein-gated inward rectifier K+ chan... -

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Basic information

Entry
Database: PDB / ID: 3syq
TitleCrystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (Kir3.2) R201A mutant in complex with PIP2
ComponentsG protein-activated inward rectifier potassium channel 2
KeywordsMETAL TRANSPORT / ion channel / potassium channel / inward rectification / sodium binding / PIP2 binding / G protein binding
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 / monoatomic ion channel complex / neuronal cell body membrane / potassium ion import across plasma membrane ...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 / monoatomic ion channel complex / neuronal cell body membrane / potassium ion import across plasma membrane / potassium channel activity / G-protein alpha-subunit binding / negative regulation of insulin secretion / presynapse / presynaptic membrane / postsynapse / axon / dendrite / cell surface / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir3.2 / 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 ...Potassium channel, inwardly rectifying, Kir3.2 / 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 / G protein-activated inward rectifier potassium channel 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.44 Å
AuthorsWhorton, M.R. / MacKinnon, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Crystal Structure of the Mammalian GIRK2 K(+) Channel and Gating Regulation by G Proteins, PIP(2), and Sodium.
Authors: Whorton, M.R. / Mackinnon, R.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 2
B: G protein-activated inward rectifier potassium channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8557
Polymers77,9522
Non-polymers9035
Water00
1
A: G protein-activated inward rectifier potassium channel 2
B: G protein-activated inward rectifier potassium channel 2
hetero molecules

A: G protein-activated inward rectifier potassium channel 2
B: G protein-activated inward rectifier potassium channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,70914
Polymers155,9034
Non-polymers1,80610
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area22320 Å2
ΔGint-123 kcal/mol
Surface area48200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.605, 208.491, 117.376
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-501-

K

21A-502-

K

31A-503-

K

41A-504-

K

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A100 - 179
2111B100 - 179
1124A203 - 225
2124B203 - 225
1224A238 - 244
2224B238 - 244
1324A260 - 308
2324B260 - 308
1426A325 - 382
2426B325 - 382

NCS ensembles :
ID
1
2

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Components

#1: Protein G protein-activated inward rectifier potassium channel 2 / GIRK-2 / Inward rectifier K(+) channel Kir3.2 / Potassium channel / inwardly rectifying subfamily J member 6


Mass: 38975.844 Da / Num. of mol.: 2 / Fragment: UNP residues 52-380 / Mutation: R201A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Girk2, Kcnj6, Kcnj7, W / Plasmid: pPICZ / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1163 / References: UniProt: P48542
#2: 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
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
Has protein modificationY
Sequence detailsUNP P48542 S260T, I313M, AND M344L ARE NATURAL VARIANTS.

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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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 50 mM HEPES sodium, pH 7.25, 0.5 M sodium chloride, 25% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.034 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.034 Å / Relative weight: 1
ReflectionResolution: 3.432→49.39 Å / Num. obs: 14690 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.063 / Χ2: 1.538 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
3.45-3.577.414611.1141100
3.57-3.727.514311.223199.9
3.72-3.897.514411.20511000.968
3.89-4.097.514531.33611000.577
4.09-4.357.514461.54111000.298
4.35-4.687.514621.8711000.183
4.68-5.157.514652.10111000.148
5.15-5.97.414731.91811000.114
5.9-7.437.414891.89111000.08
7.43-49.38611.815691.33199.70.043

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0110refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E4F

2e4f


Resolution: 3.44→49.39 Å / Cor.coef. Fo:Fc: 0.842 / Cor.coef. Fo:Fc free: 0.858 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 112.639 / SU ML: 0.78 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.77 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3227 575 4.9 %RANDOM
Rwork0.2995 ---
obs0.3006 11814 80.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 244.8 Å2 / Biso mean: 138.3704 Å2 / Biso min: 85.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 3.44→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4490 0 35 0 4525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224619
X-RAY DIFFRACTIONr_angle_refined_deg1.0191.9556290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2815578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31723.575179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50815728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0031520
X-RAY DIFFRACTIONr_chiral_restr0.0660.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213385
X-RAY DIFFRACTIONr_mcbond_it0.2571.52901
X-RAY DIFFRACTIONr_mcangle_it0.47724658
X-RAY DIFFRACTIONr_scbond_it0.45231718
X-RAY DIFFRACTIONr_scangle_it0.824.51632
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1477TIGHT POSITIONAL0.010.05
1477TIGHT THERMAL0.010.5
2621MEDIUM POSITIONAL0.360.5
2378LOOSE POSITIONAL0.335
2621MEDIUM THERMAL1.462
2378LOOSE THERMAL0.9110
LS refinement shellResolution: 3.44→3.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.457 76 -
Rfree-4 -
all-80 -
obs--7.43 %
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)
12.42711.47460.36147.8977-1.01832.7487-0.4083-0.53360.19691.1245-0.1470.9345-0.3751-0.47220.55540.60480.10660.38280.8337-0.35580.643-10.415433.0676-16.7333
21.1890.06530.112510.8283.02472.67770.06550.12260.2935-1.0134-0.53680.9212-0.4641-0.49460.47130.49340.1844-0.05660.7049-0.12790.5787-11.936233.6209-39.6322
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 377
2X-RAY DIFFRACTION2B55 - 378

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