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- PDB-2gix: Cytoplasmic Domain Structure of Kir2.1 containing Andersen's Muta... -

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Basic information

Entry
Database: PDB / ID: 2gix
TitleCytoplasmic Domain Structure of Kir2.1 containing Andersen's Mutation R218Q and Rescue Mutation T309K
ComponentsInward rectifier potassium channel 2Inward-rectifier potassium channel
KeywordsMETAL TRANSPORT / Cytoplasmic Domains of Kir2.1 / Andersen's Mutation
Function / homology
Function and homology information


Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / cardiac muscle cell action potential / relaxation of skeletal muscle / Phase 4 - resting membrane potential / magnesium ion transport / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits ...Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / cardiac muscle cell action potential / relaxation of skeletal muscle / Phase 4 - resting membrane potential / magnesium ion transport / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / membrane repolarization during cardiac muscle cell action potential / regulation of membrane repolarization / positive regulation of potassium ion transmembrane transport / inward rectifier potassium channel activity / cardiac muscle cell action potential involved in contraction / regulation of cardiac muscle cell contraction / regulation of monoatomic ion transmembrane transport / relaxation of cardiac muscle / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / intercalated disc / voltage-gated potassium channel complex / potassium ion transmembrane transport / phosphatidylinositol-4,5-bisphosphate binding / T-tubule / potassium ion transport / cellular response to mechanical stimulus / postsynaptic membrane / protein homotetramerization / dendritic spine / neuronal cell body / dendrite / glutamatergic synapse / membrane / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir2.1 / 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, Kir2.1 / 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 / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Inward rectifier potassium channel 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsPegan, S. / Arrabit, C. / Slesinger, P.A. / Choe, S.
CitationJournal: Biochemistry / Year: 2006
Title: Andersen's Syndrome Mutation Effects on the Structure and Assembly of the Cytoplasmic Domains of Kir2.1.
Authors: Pegan, S. / Arrabit, C. / Slesinger, P.A. / Choe, S.
History
DepositionMar 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_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 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inward rectifier potassium channel 2
B: Inward rectifier potassium channel 2
C: Inward rectifier potassium channel 2
D: Inward rectifier potassium channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1459
Polymers95,6334
Non-polymers5125
Water12,611700
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15150 Å2
ΔGint-67 kcal/mol
Surface area35260 Å2
MethodPISA
2
A: Inward rectifier potassium channel 2
B: Inward rectifier potassium channel 2
C: Inward rectifier potassium channel 2
D: Inward rectifier potassium channel 2
hetero molecules

A: Inward rectifier potassium channel 2
B: Inward rectifier potassium channel 2
C: Inward rectifier potassium channel 2
D: Inward rectifier potassium channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,28918
Polymers191,2668
Non-polymers1,02410
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area32270 Å2
ΔGint-156 kcal/mol
Surface area68540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.674, 98.876, 98.094
Angle α, β, γ (deg.)90.00, 130.68, 90.00
Int Tables number5
Space group name H-MC121
DetailsBiological Assembly is a tetramer

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Components

#1: Protein
Inward rectifier potassium channel 2 / Inward-rectifier potassium channel / Potassium channel / inwardly rectifying subfamily J member 2 / Inward rectifier K+ / channel Kir2.1


Mass: 23908.197 Da / Num. of mol.: 4 / Mutation: R218Q, T309K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnj2, Irk1 / Plasmid: pHis8 / Production host: Escherichia coli (E. coli) / References: UniProt: P35561
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 35% MPD, 0.1 NaPO4/KPO4, 50mM NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 66471 / Num. obs: 66107 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.086 / Χ2: 1.016 / Net I/σ(I): 8.8
Reflection shellResolution: 2.02→2.09 Å / % possible obs: 97.1 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.347 / Num. unique obs: 6428 / Χ2: 0.952 / % possible all: 99.45

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å48.96 Å
Translation2.5 Å48.96 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Cytoplasmic Domains of Kir2.1

Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / Highest resolution: 2.02 Å / SU B: 4.028 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3363 5.1 %RANDOM
Rwork0.177 ---
obs0.191 66106 99.45 %-
all-66471 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.865 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å21.13 Å2
2---0.6 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Highest resolution: 2.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6570 0 1 732 7303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226709
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9519074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9585814
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61724325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.599151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5911544
X-RAY DIFFRACTIONr_chiral_restr0.1180.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025036
X-RAY DIFFRACTIONr_nbd_refined0.2080.22840
X-RAY DIFFRACTIONr_nbtor_refined0.3120.24471
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2736
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.226
X-RAY DIFFRACTIONr_mcbond_it1.1121.54070
X-RAY DIFFRACTIONr_mcangle_it2.06626588
X-RAY DIFFRACTIONr_scbond_it3.07232658
X-RAY DIFFRACTIONr_scangle_it4.6754.52486
LS refinement shellResolution: 2.02→2.075 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 239 -
Rwork0.211 4381 -
obs-4620 94.17 %

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