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- PDB-4rue: Human K2P4.1 (TRAAK) potassium channel, G124I mutant -

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Basic information

Entry
Database: PDB / ID: 4rue
TitleHuman K2P4.1 (TRAAK) potassium channel, G124I mutant
ComponentsPotassium channel subfamily K member 4
KeywordsMETAL TRANSPORT / POTASSIUM ION CHANNEL
Function / homology
Function and homology information


mechanosensitive potassium channel activity / TWIK related potassium channel (TREK) / detection of mechanical stimulus involved in sensory perception of touch / sensory perception of temperature stimulus / temperature-gated cation channel activity / Phase 4 - resting membrane potential / potassium channel complex / cellular response to alkaline pH / stabilization of membrane potential / potassium ion leak channel activity ...mechanosensitive potassium channel activity / TWIK related potassium channel (TREK) / detection of mechanical stimulus involved in sensory perception of touch / sensory perception of temperature stimulus / temperature-gated cation channel activity / Phase 4 - resting membrane potential / potassium channel complex / cellular response to alkaline pH / stabilization of membrane potential / potassium ion leak channel activity / cellular response to temperature stimulus / outward rectifier potassium channel activity / cellular response to fatty acid / potassium channel activity / potassium ion transmembrane transport / sensory perception of pain / potassium ion transport / memory / cellular response to mechanical stimulus / identical protein binding / plasma membrane
Similarity search - Function
Two pore domain potassium channel, TRAAK / Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Potassium channel subfamily K member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLolicato, M. / Minor, D.L.Jr.
CitationJournal: Neuron / Year: 2014
Title: Transmembrane Helix Straightening and Buckling Underlies Activation of Mechanosensitive and Thermosensitive K2P Channels.
Authors: Lolicato, M. / Riegelhaupt, P.M. / Arrigoni, C. / Clark, K.A. / Minor, D.L.
History
DepositionNov 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potassium channel subfamily K member 4
B: Potassium channel subfamily K member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5188
Polymers67,2842
Non-polymers2356
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10650 Å2
ΔGint-89 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.490, 118.697, 128.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Potassium channel subfamily K member 4 / TWIK-related arachidonic acid-stimulated potassium channel protein / TRAAK / Two pore potassium ...TWIK-related arachidonic acid-stimulated potassium channel protein / TRAAK / Two pore potassium channel KT4.1 / Two pore K(+) channel KT4.1


Mass: 33641.910 Da / Num. of mol.: 2 / Fragment: UNP residues 1-300 / Mutation: G124I, N104Q, N108Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK4, TRAAK / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1163 / References: UniProt: Q9NYG8
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 8

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Sample preparation

CrystalDensity Matthews: 4.97 Å3/Da / Density % sol: 75.23 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 23% PEG400, 2% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 3, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.3→49.11 Å / Num. all: 20804 / Num. obs: 19538 / % possible obs: 100 %
Reflection shellResolution: 3.3→3.56 Å / % possible all: 99

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4I9W

4i9w


Resolution: 3.3→14.994 Å / SU ML: 1.24 / σ(F): 1.33 / Phase error: 54.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3234 1026 5.25 %RANDOM
Rwork0.2915 ---
obs0.2931 19538 95.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→14.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3887 0 6 0 3893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033988
X-RAY DIFFRACTIONf_angle_d0.6775437
X-RAY DIFFRACTIONf_dihedral_angle_d19.4852362
X-RAY DIFFRACTIONf_chiral_restr0.023637
X-RAY DIFFRACTIONf_plane_restr0.004675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.4720.47031110.48222148X-RAY DIFFRACTION79
3.472-3.68650.42951340.43652517X-RAY DIFFRACTION91
3.6865-3.96630.45591690.45652704X-RAY DIFFRACTION99
3.9663-4.35650.43641510.3562720X-RAY DIFFRACTION99
4.3565-4.96670.30121440.28392742X-RAY DIFFRACTION99
4.9667-6.18370.36881850.30392757X-RAY DIFFRACTION100
6.1837-14.99380.23941320.21862924X-RAY DIFFRACTION100

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