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- PDB-1u4e: Crystal Structure of Cytoplasmic Domains of GIRK1 channel -

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Basic information

Entry
Database: PDB / ID: 1u4e
TitleCrystal Structure of Cytoplasmic Domains of GIRK1 channel
ComponentsG protein-activated inward rectifier potassium channel 1
KeywordsMETAL TRANSPORT
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsPegan, S. / Arrabit, C. / Zhou, W. / Kwiatkowski, W. / Slesinger, P.A. / Choe, S.
CitationJournal: Nat Neurosci / Year: 2005
Title: Cytoplasmic domain structures of Kir2.1 and Kir3.1 show sites for modulating gating and rectification.
Authors: Scott Pegan / Christine Arrabit / Wei Zhou / Witek Kwiatkowski / Anthony Collins / Paul A Slesinger / Senyon Choe /
Abstract: N- and C-terminal cytoplasmic domains of inwardly rectifying K (Kir) channels control the ion-permeation pathway through diverse interactions with small molecules and protein ligands in the cytoplasm. ...N- and C-terminal cytoplasmic domains of inwardly rectifying K (Kir) channels control the ion-permeation pathway through diverse interactions with small molecules and protein ligands in the cytoplasm. Two new crystal structures of the cytoplasmic domains of Kir2.1 (Kir2.1(L)) and the G protein-sensitive Kir3.1 (Kir3.1(S)) channels in the absence of PIP(2) show the cytoplasmic ion-permeation pathways occluded by four cytoplasmic loops that form a girdle around the central pore (G-loop). Significant flexibility of the pore-facing G-loop of Kir2.1(L) and Kir3.1(S) suggests a possible role as a diffusion barrier between cytoplasmic and transmembrane pores. Consistent with this, mutations of the G-loop disrupted gating or inward rectification. Structural comparison shows a di-aspartate cluster on the distal end of the cytoplasmic pore of Kir2.1(L) that is important for modulating inward rectification. Taken together, these results suggest the cytoplasmic domains of Kir channels undergo structural changes to modulate gating and inward rectification.
History
DepositionJul 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: G protein-activated inward rectifier potassium channel 1


Theoretical massNumber of molelcules
Total (without water)24,1531
Polymers24,1531
Non-polymers00
Water2,324129
1
A: G protein-activated inward rectifier potassium channel 1

A: G protein-activated inward rectifier potassium channel 1

A: G protein-activated inward rectifier potassium channel 1

A: G protein-activated inward rectifier potassium channel 1


Theoretical massNumber of molelcules
Total (without water)96,6104
Polymers96,6104
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area11580 Å2
ΔGint-13 kcal/mol
Surface area35800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.357, 76.357, 92.164
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

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Components

#1: Protein G protein-activated inward rectifier potassium channel 1 / GIRK1 / Potassium channel / inwardly rectifying / subfamily J / member 3 / Inward rectifier K+ ...GIRK1 / Potassium channel / inwardly rectifying / subfamily J / member 3 / Inward rectifier K+ channel Kir3.1 / KGA / KGB1


Mass: 24152.568 Da / Num. of mol.: 1 / Fragment: Cytoplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnj3, GIRK1, Kga / Plasmid: pHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P63250, UniProt: P35562
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.2 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ethanol, hepes, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.08 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 20, 2003
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. all: 17035 / Num. obs: 16100 / % possible obs: 94.51 % / Redundancy: 6.7 % / Rsym value: 0.07 / Net I/σ(I): 23.02
Reflection shellResolution: 2.08→2.15 Å / % possible all: 73.32

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N9P
Resolution: 2.09→91.29 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.589 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23505 813 5.1 %RANDOM
Rwork0.19431 ---
all0.19641 15270 --
obs0.19641 15270 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.928 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20 Å2
2---1.12 Å20 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 2.09→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 0 129 1728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0211632
X-RAY DIFFRACTIONr_bond_other_d0.0020.021461
X-RAY DIFFRACTIONr_angle_refined_deg2.3781.9512204
X-RAY DIFFRACTIONr_angle_other_deg1.16133398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0085198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1770.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021803
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02340
X-RAY DIFFRACTIONr_nbd_refined0.2340.2305
X-RAY DIFFRACTIONr_nbd_other0.2720.21720
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0980.2992
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3770.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.8581.5996
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.26821618
X-RAY DIFFRACTIONr_scbond_it4.2123636
X-RAY DIFFRACTIONr_scangle_it6.6554.5586
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.145 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 47
Rwork0.276 999

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