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- PDB-5kuk: Crystal Structure of Inward Rectifier Kir2.2 K62W Mutant -

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Basic information

Entry
Database: PDB / ID: 5kuk
TitleCrystal Structure of Inward Rectifier Kir2.2 K62W Mutant
ComponentsATP-sensitive inward rectifier potassium channel 12
KeywordsMETAL TRANSPORT / METAL TRANSPORT Kir 2.2 K62W mutant structure
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 / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / monoatomic ion channel complex / potassium ion import across plasma membrane / potassium ion transport / protein homotetramerization ...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 / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / monoatomic ion channel complex / potassium ion import across plasma membrane / potassium ion transport / protein homotetramerization / membrane / identical protein binding / 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
: / ATP-sensitive inward rectifier potassium channel 12
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLee, S.-J. / Ren, F. / Heyman, S. / Yuan, P. / Nichols, C.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1 United States
American Heart Association2 United States
CitationJournal: J.Gen.Physiol. / Year: 2016
Title: Structural basis of control of inward rectifier Kir2 channel gating by bulk anionic phospholipids.
Authors: Lee, S.J. / Ren, F. / Zangerl-Plessl, E.M. / Heyman, S. / Stary-Weinzinger, A. / Yuan, P. / Nichols, C.G.
History
DepositionJul 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 4, 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
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-sensitive inward rectifier potassium channel 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,25311
Polymers39,4191
Non-polymers83410
Water3,351186
1
A: ATP-sensitive inward rectifier potassium channel 12
hetero molecules

A: ATP-sensitive inward rectifier potassium channel 12
hetero molecules

A: ATP-sensitive inward rectifier potassium channel 12
hetero molecules

A: ATP-sensitive inward rectifier potassium channel 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,01344
Polymers157,6754
Non-polymers3,33840
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 area29200 Å2
ΔGint-172 kcal/mol
Surface area54550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.695, 82.695, 182.441
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-505-

K

61A-506-

K

71A-507-

K

81A-508-

K

91A-509-

K

101A-766-

HOH

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Components

#1: Protein ATP-sensitive inward rectifier potassium channel 12 / Inward rectifier K(+) channel Kir2.2 / Potassium channel / inwardly rectifying subfamily J member 12


Mass: 39418.754 Da / Num. of mol.: 1 / Fragment: UNP residues 38-369 / Mutation: K62W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: KCNJ12 / Production host: Komagataella pastoris (fungus) / References: UniProt: F1NHE9
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: K
#3: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 4.03 Å3/Da / Density % sol: 69.46 %
Crystal growTemperature: 293.15 K / Method: evaporation / Details: tri-sodium citrate, NaCl, PEG 400 / PH range: 5.8-7.0

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→91.39 Å / Num. obs: 40670 / % possible obs: 99.6 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.32
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.675 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREP5.8.0048phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SPI

3spi


Resolution: 2→91.39 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.116 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22667 1965 4.8 %RANDOM
Rwork0.19906 ---
obs0.20038 38705 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.074 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2--1.46 Å20 Å2
3----2.93 Å2
Refinement stepCycle: LAST / Resolution: 2→91.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 35 186 2834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192806
X-RAY DIFFRACTIONr_bond_other_d0.0010.022715
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.9653830
X-RAY DIFFRACTIONr_angle_other_deg0.71836252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5895357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38423.359128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87815493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0361520
X-RAY DIFFRACTIONr_chiral_restr0.0630.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02666
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1073.3861338
X-RAY DIFFRACTIONr_mcbond_other1.1073.3831337
X-RAY DIFFRACTIONr_mcangle_it1.8845.0631680
X-RAY DIFFRACTIONr_mcangle_other1.8835.0661681
X-RAY DIFFRACTIONr_scbond_it1.2943.6521468
X-RAY DIFFRACTIONr_scbond_other1.2943.6541469
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1875.4162136
X-RAY DIFFRACTIONr_long_range_B_refined4.96227.6553319
X-RAY DIFFRACTIONr_long_range_B_other4.72827.3413237
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 148 -
Rwork0.299 2722 -
obs--94.56 %

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