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

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Basic information

Entry
Database: PDB / ID: 3syp
TitleCrystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (Kir3.2) R201A mutant
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 / inward rectifier potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / parallel fiber to Purkinje cell synapse / potassium channel activity / negative regulation of insulin secretion / presynapse ...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 / inward rectifier potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / parallel fiber to Purkinje cell synapse / potassium channel activity / negative regulation of insulin secretion / presynapse / presynaptic membrane / postsynapse / 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
: / G protein-activated inward rectifier potassium channel 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 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_label_atom_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_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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1716
Polymers38,9761
Non-polymers1955
Water00
1
A: G protein-activated inward rectifier potassium channel 2
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)156,68524
Polymers155,9034
Non-polymers78220
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area25310 Å2
ΔGint-159 kcal/mol
Surface area49300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.431, 85.431, 178.209
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
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 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.: 1 / 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / 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: 4.17 Å3/Da / Density % sol: 70.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM sodium citrate, pH 6.0, 1 M sodium chloride, 30-35% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2010
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.1→42.36 Å / Num. obs: 12081 / % possible obs: 97.6 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.108 / Χ2: 1.404 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
3.1-3.218.811801.086198.9
3.21-3.348.911901.13198.80.842
3.34-3.498.911921.17198.80.594
3.49-3.688.911891.221198.30.37
3.68-3.918.811891.306198.30.24
3.91-4.218.812071.361198.20.14
4.21-4.638.712061.658197.70.094
4.63-5.38.712151.789197.50.081
5.3-6.678.412281.803196.90.079
6.67-42.3557.912851.529192.90.053

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Processing

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

2e4f


Resolution: 3.12→42.36 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 0.13 / SU B: 37.689 / SU ML: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.92 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2958 838 6.9 %RANDOM
Rwork0.2623 ---
obs0.2646 12065 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 350.76 Å2 / Biso mean: 115.2284 Å2 / Biso min: 57.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 3.12→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 5 0 2316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222362
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9443219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7195302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87623.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.35615363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.408159
X-RAY DIFFRACTIONr_chiral_restr0.0890.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211749
X-RAY DIFFRACTIONr_mcbond_it0.7091.51513
X-RAY DIFFRACTIONr_mcangle_it1.31722419
X-RAY DIFFRACTIONr_scbond_it1.3213849
X-RAY DIFFRACTIONr_scangle_it2.3584.5800
LS refinement shellResolution: 3.116→3.197 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 42 -
Rwork0.297 744 -
all-786 -
obs--86.85 %
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)
12.87440.1106-0.2853.0971.12833.5085-0.06380.70480.1507-0.6724-0.09590.0867-0.1894-0.14420.15960.256-0.0427-0.02620.2120.07580.21287.6398-25.55264.3569
22.53731.22191.50913.58995.40310.5833-0.11850.705-0.7263-0.58920.2973-0.88420.00921.4942-0.17881.51440.03430.50421.6138-0.02910.971915.0434-42.395119.8312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 69
2X-RAY DIFFRACTION1A170 - 381
3X-RAY DIFFRACTION2A76 - 117
4X-RAY DIFFRACTION2A134 - 169

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